The Effects of Timber Harvest on the East Duncan Canal Estuary

The Tonka Timber Sale is planned for Kupreanof Island near Petersburg in southeast Alaska. Little study has been given to the effect of timber harvest on estuaries. We are providing an analysis of timber harvests on East Duncan Canal estuaries. The two main studies we observed are biogeochemical cycling and hydrological processes.


The Tonka Timber Sale is planned for Kupreanof Island near Petersburg in southeast Alaska. Little study has been given to the effect of timber harvest on estuaries. We are providing an analysis of timber harvests on East Duncan Canal estuaries. The two main studies we observed are biogeochemical cycling and hydrological processes. Alternative 4 from the U.S. Forest Service’s Tonka Timber Sale is used as a management plan to monitor the harvest of timber with adaptations for roads. Effects were found to be mixed, and direct impacts to streams and downstream at the estuary minimized with buffers. Short-term, there may be an increase in nutrients as a result of increase in temperatures; however, in the long-term, there may be a decrease in the nutrients available. Hydrologically, clear-cuts may increase run-off, yet the buffers and fast re-vegetation minimize changes. Sedimentation is of more concern, particular with reference to roads constructed. Estuaries may see a disruption in the food chain due to sedimentation or nutrient pulses, or perhaps through a negative impact on salmon. Alternative 4 from the U.S. Forest Service’s Tonka Timber Sale Final Environmental Impact Statement will be used as the management plan, with our recommendation for ensuring that 1) buffers, 2) controlling for landslides and sedimentation from roads, and 3) culvert placement for fish passage be given emphasis. The cost of implementing roads via Alternative 4 is approximately 3.9 million dollars, and we believe that monitoring the estuary will be $6200/month. We will monitor temperature, salinity, acidity, turbidity, and the input of nutrients in the estuary. Salmon populations are critical to monitor. We are not expecting any major estuarine effects. The health of the salmon run is found to be the biggest issue that could impact estuarine function.


In this paper, we will examine the effects of the Tonka timber sale on estuaries at the head of east Duncan Canal on Kupreanof Island, with an emphasis on protecting the health of the estuary. The Tonka Timber Sale is planned for Kupreanof Island near Petersburg in southeast Alaska. Little study has been given to the effect of timber harvest on estuaries. We are providing an analysis of timber harvests on East Duncan Canal estuaries. The two parameters we assessed are biogeochemical cycling and hydrological processes. Alternative 4 from the U.S. Forest Service’s Tonka Timber Sale Final Environmental Impact Statement (USDA, 2012) is used as a management plan to monitor the harvest of timber with adaptations for roads. We chose Alternative 4 because it was selected as the preferred alternative by the Forest Service allowing our team to focus our analysis on estuarine effects rather than harvest practices. After completion of our analysis, we will give recommendations to improve upon the management plan.

Timber Industry in Southeastern Alaska

Timber traditionally has been a part of our local economy here in Petersburg, AK. During the early 1900’s, nine mills were operating. The first one, owned by O.P. Brown employed 40-60 men. Later, another mill opened, employing 35-40 people (Mackovjak, 2010). Today there are only three small mills in Petersburg; however, even at that, most timber sales purchased from the US Forest Service do not go to local mills. In 2005, less than one percent of Petersburg’s workforce was employed in the timber industry (Headwaters Economics, 2005).

Petersburg is commonly known as a Norwegian fishing town in southeastern Alaska with a population of almost three thousand. The health of the natural resources is a crucial piece of the economy because roughly 70% of the city’s revenue is tied to it via fishing. Within Petersburg, 80 million pounds of fish are landed annually, earning citizens approximately 67 million dollars (“CFEC,” 2011). Fisheries resources that are so vital to our town they need to be maintained, while at the same time we would like to diversify Petersburg’s economy by supporting jobs in the timber industry.

According to the article “Alaska Timber,” before Alaska was purchased in 1867 timber was primarily used for mining and fishing. In 1905 the Forest Service was created, and two years later the Tongass National Forest was established. This forest encompasses 93% of timberland in Southeast Alaska. When the Forest Service offered 50-year timber contracts to harvest wood on the Tongass, two mills were created during the fifties: the Ketchikan Pulp Company, and the Sitka Pump Mill. By 1997, both the Ketchikan and Sitka mills closed down (“Alaska Timber,” 2012). During the time from 1990 to 2007 timber harvests plummeted by 96% from 471 million board feet to 18.7 million, and timber-related jobs declined by 87% from 3,543 to 265 (Alexander et al., 2010).


The US Forest Service evaluates environmental impact(s) of timber harvest on terrestrial and freshwater systems; however, not as much work has been done to study the effects on estuaries. Estuaries are of crucial importance because they transfer organisms, nutrients, oxygen, sediments and waste (NOAA, 2008), and is the region where the river and ocean converge, creating a transitional zone (Krause, 1999). Factors that affect mixing include: speed and wind direction, tides, estuary shape, speed and water volume. They are vital to many forms of marine and land based species for habitat, breeding and rearing grounds, and habitat. Estuaries can also have economic value because of the species that are harvested from estuarine waters or that originated from them, such as salmon and other fish. The annual revenue from commercial fishing in estuaries in the U.S. is 4.3 billion dollars (NOAA, 2008). Estuaries are one of the most productive ecosystems on earth (Plujm, 2008).

For our analysis, we considered the effects of harvest on all watersheds that drain into the estuary at the head of Duncan Canal, including the large Mitchell and Duncan Creek watersheds (Figure 1). Of the four primary estuarine types: salt-wedge, fjords, slightly stratified, and vertically mixed estuaries (NOAA, 2008), Duncan Canal is a vertically mixed estuary. This occurs when a slow freshwater river and fast saltwater converge, where there is a large difference between low and high tides. The estuary types are normally found in large, shallow estuaries (NOAA, 2008).

Due to the mixing, the salinity is, hypothetically, consistent no matter the depth. The Duncan Canal estuary is classified by the National Wetland Inventory as an intertidal estuary, with an unconsolidated shore that is regularly flooded (E2USN, Figure 1) (U.S Fish and Wildlife).

Figure 1: East Duncan Canal Study Area Image on left shows National Wetland Inventory classification, image on right shows satellite imagery of estuarine study area (Google Earth, 2012).

Timber harvest effects from harvest, downstream…

In our analysis of the effects of Alternative 4 timber harvest, we will discuss 1) the short and long-term changes to the terrestrial environment following harvest; 2) the related impacts of harvest to the freshwater ecosystem; and 3) extrapolate the possible effects upon the estuary. In this study, anadromous Pacific Salmon (Oncorhynchus sp.) and riparian red alder (Alnus rubra) play a key ecological role in this process.

Terrestrial Impacts

The removal of vegetative biomass is the most visible effect of clear-cut harvest and road construction, thus directly removing available nutrients from the system. The absence of a canopy following clear-cut produces some short-term effects. Nutrient cycling is directly affected by temperature, as temperature increases it further increases the rate of nutrient cycling. In the absence of forest canopy, thermal radiation increases soil temperature, which increases the flux of carbon either into the atmosphere or into the water. Again, re- vegetation occurs quickly in southeastern Alaska and is substantial enough to remove this temperature effect in the short-term. While we think that this would increase labile nitrogen, phosphorus and carbon, we do know that our soil is rich in iron, which bonds with the carbon present and keeps it locked in the soil (D’Amore, 2012).

Additional short-term impacts include changes to water movement in the absence of a forest canopy. Research conducted by Harr and Coffin (1992) shows that there is less precipitation interception by forest canopy after timber harvest. This results in significant rises in peak flow for the watershed as water hits the soil and moves directly to the streams (Figure 2). Snow will likewise affect the peak flow during rain-on-snow conditions. Rain-on- snow conditions occur when snowpack increases with the lack of canopy interception (Harr and Coffin, 1992). In our region, the Alaska Current supplies warm winds that turn snow into rain, quickly melting snowpack.

Figure 2: Snowpack depth before and after timber harvest showing a significant increase in peak run- off with timber harvest (Harr and Coffin, 1992)

In contrast to the increased capture of precipitation, Ingwersen (1985) found that the fog hangs closer to the ground and does not become “fog drip.” Fog drip occurs when tree stands intercept fog and the moisture is collected on the branches. After collection, the condensation drips down to ground level contributing to run-off. The loss of fog drip only becomes a factor in the short-term; however, as at the end of about six years the vegetation is able to recapture this precipitation (Ingwersen, 1985).

Soil erosion will take place at an increased rate due to the absence of root systems. These effects start with less interception of rain in the watershed. Slowly, the runoff builds and pushes sediments into the streams. This could cause sedimentation, which can diverge or hinder stream flow. The chances for landslides increase due to the removal of roots because of decay (Gray, 2009). The roots decompose or are taken out of the ground and create ‘pipes’ that filter water from increased precipitation into the landmass contributing to internal and seepage soil erosion (Gray, 2009). These factors combined create the perfect scenario for a landslide. Eroded land weighed down by excess precipitation standing precariously on a slippery surface created by the pipes will almost definitely increase the probability of a landslide occurring to the point of the event actually taking place (Gray, 2009).

Freshwater Impacts

The direct effect to the aquatic environment as a result of clear-cut harvest is moderated by the inclusion of buffers. A buffer is a set area around a stream or river in which trees cannot be harvested (Emil Tucker pers comm, 2012). This buffer helps to keep sediment from running into the streams, as well as to maintain shade and structure. Buffer zones are a set distance from the water flow onto the landmass where trees cannot be cut, with the size of the buffer dependent on the stream classification (Emil Tucker pers comm, 2012). The Duncan Creek and Mitchell Creek watersheds contain anadromous fish species, and as a result they have a 100-meter buffer on both stream banks (USFS, 2012).

Red alder is an important riparian tree species because it has nitrogen-fixing bacteria that live in the roots. These bacteria take the inorganic nitrogen form and convert it to a useable organic form. This organic nitrogen is then taken from the soil for use in both terrestrial and aquatic ecosystems. If these nitrogen- fixing bacteria were to be removed from the ecosystem, productivity would decrease due to the lack of nitrogen availability. The absence of nitrogen would negatively affect the diversity of aquatic invertebrates due to the lack of nitrogen brought into the system (Table 1) (Hernandez et al., 2005).

Table 1: Nitrogen level in a comparison of leaf tissues to invertebrates. (Wipfli, 1997)

Regarding changes in hydrology, peak flow events, while significantly different when comparing harvest to non-harvest sites, cause little change in stream stage (Harr and Coffin, 1992). With respect to base flows, Grant et al. (2008) found that the streams had lower base flows during the summer months. This could also contribute to warmer temperatures in-stream that could then affect invertebrates and salmon.

Sedimentation could still be a problem. Increased run-off brings with it sediment from the harvest areas (Harr and Coffin, 1992). According to Emil Tucker (2012), roads are crucial to sedimentation. Many engineers, when looking at crossing multiple small streams with a road, funnel multiple streams along the side of the road into a larger stream as a cost effective measure. It is simpler to build a single culvert than struggle with 5-10 smaller culverts. The streams amassed in this manner provide a ‘fire hose’ type effect, which hinders the ability for fish to swim upstream and contributes to sedimentation. Sediment entering the water flow may cause a variety of problems, such as decreasing available sunlight for photosynthesis and possibly smothering salmon egg and other aquatic organisms in the gravel (Emil Tucker pers comm, 2012).

In-stream habitat changes are more difficult to assess due to the variability in vegetative communities – due to both buffers and stand regeneration. In the absence of old- growth timber, such as Sitka spruce (Picea sitchensis) and Western hemlock (Tsuga heterophylla), available habitat for fish, for example, decreases. When new-growth comes in, dies, and falls into the river, it decays much quicker than the old-growth. This means it does not allow for fish to have a long-term shelter, which can cause a depression in fish biomass due to factors such as predation and rearing habitat (Emil Tucker pers comm, 2012).

According to Hernandez (2005), invertebrate density is directly influenced by habitat, specifically the type of substrate as well as light levels. He found that in ecosystems without timber harvest, substrate is varied with woody, leafy, and rocky substrate, which produces high invertebrate diversity. When the vegetative resources are taken out, however, substrate is limited to the leafy and rocky substrates resulting in lower species diversity. While the increased light will help facilitate growth, the lack of woody substrate will limit the growth and diversity of freshwater invertebrates (Table 1) (Hernandez, 2005). Medhurst et al. (2010), found that new growth changes the freshwater biota. In forests that have had a history of coniferous growth, this change to deciduous riparian growth can increase algae- eating invertebrates at the expense of the carnivorous inverts.

Studies have shown the importance of Pacific salmon to ecosystem function within and beyond the freshwater stream (Figure 3) (Chaloner et al., 2004, Heintz et. al., 2010, Martin et. al, 2010). When salmon swim upstream to spawn, their carcasses decompose, releasing important limiting resources such as carbon and nitrogen. Other consumers drag the carcasses up into the terrestrial environment, spreading the marine-derived nutrients. In the presence of salmon carcasses, all trophic levels incorporated marine- derived nitrogen (range, 22–73% of total nitrogen) and carbon (range, 7–52% of total carbon?) (Chaloner et al, 2002). This is shown in the increase of floral and faunal biomass in the forests surrounding the stream/estuary (Table 2) (Chaloner et al, 2002).

Figure 3: Comparison of streams with and without marine-derived nutrients: ammonium, nitrate, phosphorus, and DOC (Chaloner et al., 2004)

In summary, there are several potential changes that could happen to stream productivity if timber were to be harvested. This includes: a change in populations of invertebrates, a short-term increase in nutrient availability from the clear-cut site to a long- term decrease, a change in suitable habitat, as well as possible changes in flows and temperatures and sedimentation. Buffers mediate most of these possible negative effects;  however, we have little understanding of change in the nutrient balance and impacts to the fishery resource.

Table 2: Comparison between organisms and their percent of marine-derived nutrient (Chaloner et al, 2002)

Estuarine Effects

Individual streams will experience only small effects as a result of timber harvest; however, with road construction throughout the area and multiple clear-cuts, the combined effect could be more substantial. Once we harvest timber from the East Duncan area, we could see a cumulative impact in the Duncan Canal estuary from harvest in the Duncan Slough, and Duncan and Mitchell Creek watersheds. These cumulative effects could include: a change in nutrient and terrigenous input into the Duncan Canal estuary, a change in aquatic invertebrates, a resulting change in the food web and a possible decrease in salmon returns, and increased erosion. The net result is increased sediment in stream, and sediment washed out to the estuary where it has a potential for changing benthic habitats and or possibly smothering benthic organisms.

Biogeochemical cycling comes into play because more of the nutrients get washed out with the removal of biomass. When trees are taken out of the equation due to timber harvest, the nutrient cycling process is disrupted. We should see a short-term pulse of nutrients caused by processes such as leaching and increased temperatures that increase productivity. As far as ecosystem effects, the short-term effect can cause a bloom in phytoplankton, which increases energy availability throughout the trophic levels of the food web. In the long term, however, we may see a drawn out decline in population trends due to the depletion of resources. The long-term effects could cause a decline in overall productivity through changes in habitat and nutrient cycling. This decline would be due to the processes of biomass removal and road-building, which changes the characteristics of the habitat. Possible decreases in invertebrate population may also decrease the salmon returns in Mitchell and Duncan Creek and Duncan Slough, because salmon smolt may not have as much food available as usual.

Timber harvest would have a limited effect on the amount of dissolved organic carbon being washed into the aquatic environment in the long run (D’Amore, 2012). The effects, however, will be seen through carbon input through tree decomposition in the water system. This will cause a decrease in organic carbon that is available to organisms in the East Duncan estuary.

All of the afore-mentioned factors could be seen in Duncan and Mitchell Creek, as well as Duncan Slough. In the eastern portion of Duncan Canal, the cumulative impact could be visible. These impacts include decreased nutrient outflow from Duncan Creek, Mitchell Creek, and Duncan Slough, decreasing numbers of salmon fry migrating out to saltwater, a disruption in plankton biomass due to insufficient nutrient availability accompanied by a decline in the biomass of higher trophic levels, and a disruption in cyclical processes in this estuarine system, (e.g the salmon cycle).

Management Plan

Our management plan uses Alternative 4 of the Tonka Timber Sale (USDA, 2012) as the core of our proposal. The details of this alternative are found in the Final Environmental Impact Statement (FEIS). This area includes 251 square kilometers on the southern end of the Lindenberg Peninsula (Figure 4). By using this alternative, the Forest Service plans to avoid entering roadless areas and expects to harvest approximately 0.635 million board kilometers (MBK) of timber on 8.4 square kilometers of land using conventional and helicopter yarding systems. In this alternative, the FS will be building 15 kilometers of road of which 12.2 kilometers will be temporary (USDA, 2012).

Figure 4: Location of Alternative 4 (USDA, 2012).

According to the Tonka Timber Sale FEIS, for transportation, linear grading road construction will be used, which will close when harvesting ends. Rock quarries must be used, but the area footprint should not exceed 0.02 square kilometers. To transport wood: barges, log rafts, and the existing equipment ramp should be used. To keep sites safe and protect the environment, buffers will be placed along streams (USDA, 2012).

Based on the analysis of the possible impacts to the eastern Duncan Canal estuaries, we have determined that the following objectives are the most critical when implementing the timber sale:

1. It is important to limit and manage the effects to the Class I streams in the Tonka Timber Sale. There are approximately 134 km of Class I streams (USDA, 2012), in which anadromous fish, such as salmon, spawn. Stream buffers are critical for controlling erosion and maintaining the integrity of the habitat along the stream corridor.

2. Managing to decrease sedimentation from both road systems and landslides is another important goal when implementing timber harvest.

3. When building roads the building of culverts will be inevitable, we just have to make sure we build them to allow fish passage, and also take into account the effects of funneling smaller streams into a ‘fire hose’.

Monitoring Plan

To ensure that the Tonka Timber Sale has minimal effects on the estuaries of the Duncan Canal, we must implement a monitoring plan in collaboration with the US Forest Service. The Forest Service is charged with monitoring soil erosion from landslides and roads, changes in vegetative communities and freshwater and invertebrate fish populations on the terrestrial side of the equation (USDA, 2008). Our monitoring plan is developed for the saltwater side of the equations and will be implemented by the Alaska Department of Fish and Game. Estuarine monitoring would include outflow, pH, turbidity, salinity, temperature, nitrogen, phosphorus and dissolved organic carbon (EPA, 2012).

Additionally, we will monitor plankton and salmon abundance in each watershed. We have shown that salmon are critical to ecosystem health; therefore, the monitoring of salmon runs is very important as well. We propose monitoring the movement of salmonid fry to the ocean, along with population fluctuations.

Monitoring will occur at Duncan and Mitchell Creek estuaries, as well as Duncan Slough. Sampling will occur bimonthly. When starting our monitoring plan, we found it useful to have a comparative estuary with which to compare negative and positive aspects.

Comparative Estuary

We chose the Sequim Bay estuary and connected watershed as an example of what happens when overharvest occurs. Sequim Bay is an estuary on the Olympic Peninsula in Washington. We chose Sequim Bay because the estuary is protected and had past timber industry. Our estuary has the potential to be damaged like Sequim Bay if our industry is improperly managed.

This area was heavily clear-cut throughout most of 1800-1950 (“Sequim Bay”). This heavily damaged the ecosystem. Also, gear and building materials were left behind and severely hindered both water flow as well as biological life and growth. This is the worst- case scenario that could happen without proper management. If the worst-case scenario should occur, soil and timber restoration must take place. As with every restoration project, the results will be delayed in onset. The restoration process was completed in Sequim Bay in 2005, after years of restoration (“Sequim Bay”).

An increased human population was beneficial to the Sequim Bay estuary, but only after it was cleaned up by the Jamestown S’Klallam tribe post timber harvest (“Sequim Bay”). It is now used for tourism and fishing. Having an increased human population would have both negative and positive effects for the Duncan Canal Estuary. An increased population would create competition for the timber industry versus using the area for tourism/fishing, but it would increase interest and variety of workers. While this is unlikely, the potential for additional harvest (there has been previous timber harvest in these same watersheds) could indeed put the estuary at greater risk to cumulative impacts.

Timber Industry Economics

The Southeast Alaska timber industry has supplied southeast Alaska with both employment and development opportunities since the 1900’s. The timber industry originally provided 3,450 jobs, which was reduced to 450 by 2002 (Erskine, 2004). A functional timber industry could recreate some of these jobs and boost local economies (Colt et al., 2007). In conjunction with trying to provide more available jobs, we must ensure our timber proposal will not affect fishermen economically. In 2001, the Petersburg-Wrangell area had 369 fishermen who held permits. They landed almost 80 million pounds with a gross earning of about 67 million (“CFEC,” 2011).

During the 1990’s, the Alaska Pulp and Ketchikan Pulp Company started to slow, affecting operations in Ketchikan, Sitka, and Wrangell. This resulted in the loss of jobs, placing stress on communities. Seasonal logging activities in other local communities declined as well. From 1993 to 2002, Southeast’s employment increased 5.5% by an addition of 1,849 jobs. Although this seems great, it’s slightly misleading. When 5.5% is broken down, Prince of Wales, Outer Ketchikan, and Wrangell-Petersburg lost almost 1400 jobs, but Juneau added about 2,700 jobs (Colt et al., 2007).

The decline in these mills may correlate with logging costs. There are many variables that add to the cost of producing a thousand board feet (304.8m) of lumber. These costs include; pre-commercial thinning (PCT), commercial thinning (CT), grounding/shoveling costs, shipping costs, log transfer facilities and road haul costs (Alexander and Henderson, 2012).

Table 3: Comparison of the Alternatives cost (USDA, 2012)

Table 3 shows the Forest Service’s proposed Tonka Timber Sale plan costs, of which Alt. 4 is the preferred alternative (USDA, 2012). These costs represent the possible expenditures and income of our proposed plan. Alt. 4 will have an estimated direct project income of 7.6 million dollars, with the total project costing two million. This alternative will also provide 154-183 direct jobs annually, as well as many indirect jobs. For transportation, the 15 kilometers of road will cost about 1.9 million dollars in road construction, for a total project cost of 3.9 million (USDA, 2012).

In addition to the Forest Service project costs, the monitoring for estuary health is estimated to cost 10,080 annually. Alaska Department of Fish and Game will employ 2 Fishery Tech II’s at $235 a day. It will cost $270 a day for sampling. Water samples will cost $30 a sample for nitrogen, phosphorus, and DOC (Price List, 2012).


After reviewing data, we conclude that the Tonka Timber Sale will have minimal impacts on the estuarine ecosystem while benefitting the economy in southeast Alaska. We may see some cumulative effects on the East Duncan Canal estuary, but the impacts will be relatively small. We strongly recommend that buffers be placed on all fish streams, as we found that the effects of sedimentation will be minimized. Buffers would also moderate changes in the nutrient cycles. Although buffers help prevent all these things that could result negatively, we still need to monitor soil erosion in the case of a landslide occurring. Furthermore we found that road construction has a large effect on hydrology and fish passage. Installation and removal of the culverts is the main concern they cause. They would also have to reach Forest Service specifications so as to not hinder fish travel. We would have to monitor our road building because of the culverts crossing streams.

Not only have we learned that current implementation of timber harvest practices are important for managing estuarine health, but natural processes are also at work to maintain the integrity of the estuary. Natural tidal variations further reduce possible effects due to the ‘flushing’ that happens twice daily in our estuary. The tidal range is so large that harvest level effects are swept out of the estuary returning it to equilibrium. The Sequim Bay comparative watershed illustrated what could happen if timber harvest were to occur at a much larger scale. At current harvest levels, our biggest concern is the impact to salmon returns — the most significant foreseeable effect.


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The Effects of Timber Harvest on the East Duncan Canal Estuary

The Tonka Timber Sale is planned for Kupreanof Island near Petersburg in southeast Alaska. Little study has been given to the effect of timber harvest on estuaries. We are providing an analysis of timber harvests on East Duncan Canal estuaries. The two main studies we observed are biogeochemical cycling and hydrological processes.

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