Understanding how aquatic species and function in rivers are affected by land use and natural resource management is a primary concern of ecology and conservation science. This dissertation research aims to better understand the effects of fisheries management practices, specifically salmonid stocking, on stream environments. To accomplish this, I used large scale and long-term fisheries and habitat datasets, field collected biological and environmental data, and a suite of statistical analysis and modelling techniques. I found that salmonid stocking programs in New York can affect native species communities and ecosystem function through pathways that are often unrecognized or have not yet been fully studied. These results show that nonnative salmonid stocking can have a strong influence on the functioning of ecosystems through effects on nutrient cycles and impacts to invertebrate communities, suggesting that fisheries supported by the introduction of nonnative, hatchery raised fish should be considered in terms of impacts to ecosystem function.