If you are out in the woods and discover the foundation and walls for a house without a roof, would you expect anyone to be living there?
Without a roof, someone may come to visit from time to time, but not stay long. Think of cover in a stream akin to a roof on a house. Things that provide cover for stream organisms such as fish include rocks, over-hanging banks, fallen trees, logs, branches and debris jams.
Logs can scour out fine sediments in the middle of the channel and trap them along the banks, exposing gravel which provides habitat for spawning.
Logs can create pools, which provide resting habitat and refuge from extreme temperatures. In addition, fallen trees and logs also create cover and provide camouflage for fish.
Branches from trees and logs trap leaf litter flowing downstream, which serves as food for aquatic insects. Submerged logs also provide surfaces for algae and aquatic insects to attach, such as these diatoms (golden-brown algae) and case-building caddisflies, which fish eat.
When fallen trees, broken logs and debris jams are removed from a stream to “clean it up,” we expect the stream to become more uniform in channel shape and lose these diverse habitats. The loss of debris jams created by fallen trees and branches also reduces surface area for food and cover.
I have seen sport-fishing groups post Internet announcements and photographs of stream cleaning efforts whereby logs, branches, and debris jams are removed to promote fishing. An example of this is shown in the before (6/19/2013) and after (9/16/2013) photographs of wood removal near the mouth of Big Brook, a tributary stream of the Wild and Scenic Namekagon River which is known for its brook trout fishery.
While log removal may reduce the chance of fishing line entanglement or provide better passage of canoes or kayaks, it also reduces available forage and cover for fish as well as resting habitat for other organisms such as turtles. A best management practice to improve stream habitat for fisheries is to leave log and debris jams alone unless they threaten human infrastructure. These features can also be added back to the stream landscape to improve fish habitat by conducting stream restoration projects.
Additional reading on the topic:
D.B. Booth, D.R. Montgomery, and J.P. Bethel, 1997, Large woody debris in urban streams of the Pacific Northwest: in Roesner, L.A., ed., Effects of watershed development and management on aquatic ecosystems: Engineering Foundation Conference, Proceedings, Snowbird, Utah, August 4–9, 1996, pp. 178-197.
Chin, A., et al. 2008. Perceptions of wood in rivers and challenges for stream restoration in the United States. Environmental Management 41(6): 893-903.
Dolloff, C.A., and M. L. Warren Jr. 2003. Fish relationships with large wood in small streams. American Fisheries Society Symposium 37: 179-193.
Entrekin, S.A., J.L. Tank, E.J. Rosi-Marshall, T.J. Hoellein, and G.A. Lamberti. 2009. Response of secondary production by macroinvertebrates to large wood addition in three Michigan streams. Freshwater Biology 54(8): 1741-1758.
Hilderbrand, R.H., A.D. Lemly, C.A. Dolloff, and K.L. Harpster. 1998. Design considerations for large woody debris placement in stream enhancement projects. North American Journal of Fisheries Management 18: 161-167.