Mercury (Hg) contamination is an issue of national concern, affecting both wildlife and human health. The U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program, in association with the USGS Toxic Substances Hydrology Program and the USGS National Research Program, has initiated two levels of studies to investigate Hg contamination of the Nation's streams: reconnaissance and detailed studies. Reconnaissance studies entailed one-time sampling events at 266 stream sites across the Nation. Detailed studies entailed intensive spatial and temporal sampling of a small number of streams across the Nation in an effort to develop a more complete, process-level understanding of benthic Hg geochemistry and the underlying factors controlling it. This report summarizes the sampling methods used for the collection and processing of streambed sediment and pore water in association with both of these study levels. Bed-sediment characteristics, such as organic content and grain size, strongly influence Hg geochemistry; detailed characterization of these constituents within a stream reach will allow for the extrapolation of related Hg biogeochemical constituents to the reach scale.