Mercury studies conducted as part of the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program have included nationwide reconnaissance samplings of hundreds of stream sites, as well as detailed, process-oriented research at selected sites. These reconnaissance and detailed studies are intended to provide a better understanding of methylmercury bioaccumulation in stream ecosystems over a range of environmental settings. This publication describes trace-element-clean techniques used for collection and processing of aquatic invertebrates and fish to be analyzed for total mercury, methylmercury, and stable isotopes as part of NAWQA studies.