Mercury is a globally distributed pollutant that threatens human and ecosystem health. Even protected areas, such as national parks, are subjected to mercury contamination because it is delivered via atmospheric deposition, often after long-range transport. In aquatic ecosystems, certain environmental conditions can promote microbial processes that convert inorganic mercury to an organic form (methylmercury). Methylmercury biomagnifies through food webs and is a potent neurotoxicant and endocrine disruptor. This dataset contains data on the length, mass, and muscle total mercury concentration of Brown Trout (Salmo trutta) and Rainbow Trout (Oncorhynchus mykiss) collected from the Colorado River in Glen Canyon National Recreation Area (GLCA) and Grand Canyon National Park (GRCA), and Bright Angel Creek in GRCA.