Three Oregon reservoirs were evaluated for environmental parameters affecting mercury (Hg) dynamics and bioaccumulation in fish using an ecoregion approach. Ecoregions are distinguished by topography, geology, soil type and composition, and land use patterns. We examined: pH, dissolved oxygen, hardness, conductivity and concentration of Hg ([Hg]) in water; and complexing agent concentrations, organic content, inorganic and organic [Hg] in sediments; and [Hg] in three fish species. [Hg] in water was below detection (0.1 μg/L) in most water samples from the three reservoirs; in samples above detection, we reasoned that Hg was predominantly in the particulate fraction. Hg in sediment was only found consistently in the inorganic state; organic mercury was below detection (0.2 ng/g) in 83% of sediment samples. Muscle [Hg] in fish over 4 years old was above the FDA limit of 1.0 μg/g wet weight, and more than 90% of the Hg in all fish was organic mercury. [Hg] in lateral muscle was similar between smallmouth bass (Micropterus dolomieu) in Owyhee Reservoir and largemouth bass (Micropterus salmoides) in Cottage Grove Reservoir; rainbow trout (Salmo gairdneri) from Ochoco Reservoir had significantly lower levels of Hg. It is concluded that, although ecoregion parameters alone do not explain mercury dynamics, they may influence the methylation rate in areas of similar Hg loading rates.