| 2023 | "Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river" in Journal of Heredity |
| 2022 | "Estimating Macroinvertebrate Biomass for Stream Ecosystem Assessments" in International Journal of Environmental Research and Public Health |
| 2022 | "Region-Specific Interactions of Forests and Fish in North America" in American Fisheries Society Symposium |
| 2018 | "Rivers and Streams: Physical Setting and Adapted Biota" in Reference Module in Earth Systems and Environmental Sciences |
| 2017 | "Fisheries and aquatic resources of the Prairie Creek Watershed, Redwood National and State Parks" in USGS Publications |
| 2016 | "Life History Diversity in Klamath River Steelhead" in Transactions of the American Fisheries Society |
| 2014 | "Potential Fitness Benefits of the Half-Pounder Life History in Klamath River Steelhead" in Transactions of the American Fisheries Society |
| 2013 | "Flow variation and substrate type affect dislodgement of the freshwater polychaete, Manayunkia speciosa" in Freshwater Science |
| 2012 | "Invertebrate assemblages in the lower Klamath River, with reference to Manayunkia speciosa" in California Fish and Game |
| 2012 | "Movement of Resident Rainbow Trout Transplanted below a Barrier to Anadromy" in Transactions of the American Fisheries Society |
| 2011 | "Selection of Spawning Sites by Coho Salmon in a Northern California Stream" in North American Journal of Fisheries Management |
| 2010 | "Lab Rearing of a Freshwater Polychaete (Manayunkia speciosa, Sabellidae) Host for Salmon Pathogens" in Northwest Science |
| 2010 | "Carcass Addition Does Not Enhance Juvenile Salmonid Biomass, Growth, or Retention in Six Northwestern California Streams" in North American Journal of Fisheries Management |
| 2008 | "Rivers and Streams: Physical Setting and Adapted Biota" in Encyclopedia of Ecology |
| 2008 | "Rivers and streams: Ecosystem dynamics and integrating paradigms" in Encyclopedia of Ecology |
| 2007 | "Relationship Between Productivities of Salmonids and Forest Stands in Northern California Watersheds" in Western Journal of Applied Forestry |
| 2005 | "The inadequacy of the fish-bearing criterion for stream management" in Aquatic Sciences |
| 2005 | "Effects of riparian canopy opening and salmon carcass addition on the abundance and growth of resident salmonids" in Canadian Journal of Fisheries and Aquatic Sciences |
| 2005 | "Linking Forests and Fish: The Relationship Between Productivities of Salmonids and Forest Stands in Northern California" in AGU Spring Meeting |
| 2004 | "Periphyton response to increased light and salmon carcass introduction in northern California streams" in Journal of the North American Benthological Society |
| 2002 | "The contribution of suspended organic sediments to turbidity and sediment flux" in Proceedings, 8th Federal Interagency Sedimentation Conference |
| 2002 | "Channel-floodplain coupling in the Kissimmee River, Florida (USA): invertebrate movement and fish feeding" in Vereinigung fur theoretische und angewandte Limnologie |
| 2001 | "Review of Wildstream: a natural history of the free flowing river" in Fisheries |
| 2000 | "Profitable stream positions differ for brook trout and cutthroat trout" in Wild Trout VII. Management in the New Millenium: are we ready? |
| 1999 | "Establishing baseline seagrass parameters in a small estuarine bay" in Seagrasses: Monitoring Ecology, Physiology, and Management |
| 1999 | "Evaluation of the restoration of the Kissimmee River in South Florida" in The natural history of the lower Tennessee and Cumberland River valleys |
| 1998 | "Are native brook charr and introduced rainbow trout differentially adapted to upstream and downstream reaches?" in Ecology of Freshwater Fish |
| 1998 | "A case for inside out (pathogenic) population control in a stream insect" in SIL Proceedings, 1922-2010 |
| 1998 | "Proactive responses to human impacts that balance development and Atlantic salmon (Salmo salar) conservation: an integrative model" in Canadian Journal of Fisheries and Aquatic Sciences |
| 1998 | "Effect of Temperature and Macrohabitat on Interspecific Aggression, Foraging Success, and Growth of Brook Trout and Rainbow Trout Pairs in Laboratory Streams" in Transactions of the American Fisheries Society |
| 1997 | "Microhabitat Selection by Native Brook Trout and Introduced Rainbow Trout in a Small Pennsylvania Stream" in Journal of Freshwater Ecology |
| 1992 | "Interactions between Native Brook Trout and Hatchery Brown Trout: Effects on Habitat Use, Feeding, and Growth" in Transactions of the American Fisheries Society |
| 1990 | "Nonconcordance of drift and benthic activity in Baetis" in Limnology and Oceanography |
| 1989 | "An assessment of short-term depletion of stream macroinvertebrate benthos by drift" in Hydrobiologia |
| 1989 | "Shredders and Riparian Vegetation" in BioScience |
| 1988 | "Do pathogens regulate stream invertebrate populations?" in SIL Proceedings, 1922-2010 |
| 1988 | "Toward a functional classification of stream invertebrate drift" in SIL Proceedings, 1922-2010 |
| 1987 | "Stream Management: Emerging Global Similarities" in Ambio |
| 1986 | "Influence of Habitat Manipulations on Interactions Between Cutthroat Trout and Invertebrate Drift" in Ecology |
| 1985 | "Prey availability and foraging behavior of cutthroat trout in an open and forested section of stream" in SIL Proceedings, 1922-2010 |
