Artisanal and small-scale gold mining (ASGM) in Madre de Dios, Peru, continues to expand rapidly, raising concerns about increases in loading of mercury (Hg) to the environment. We measured physicochemical parameters in water and sampled and analyzed sediments and fish from multiple sites along one ASGM-impacted river and two unimpacted rivers in the region to examine whether Hg concentrations were elevated and possibly related to ASGM activity. We also analyzed the 308 fish samples, representing 36 species, for stable isotopes (δ15N and δ13C) to estimate their trophic position. Trophic position was positively correlated with the log-transformed Hg concentrations in fish among all sites. There was a lack of relationship between Hg concentrations in fish and either Hg concentrations in sediments or ASGM activity among sites, suggesting that fish Hg concentrations alone is not an ideal bioindicator of site-specific Hg contamination in the region. Fish Hg concentrations were not elevated in the ASGM-impacted river relative to the other two rivers; however, sediment Hg concentrations were highest in the ASGM-impacted river. Degraded habitat conditions and commensurate shifts in fish species and ecological processes may influence Hg bioaccumulation in the ASGM-impacted river. More research is needed on food web dynamics in the region to elucidate any effects caused by ASGM, especially through feeding relationships and food sources.