We examined the influence of heavy metal pollution from an abandoned mine on benthic macroinvertebrates, at population and community levels, and the potential amount of food available for drift-feeding fish in northern Japanese streams. We studied multiple polluted and unpolluted sites with similar longitudinal positions to avoid problems caused by upstream–downstream comparisons. The ranges of zinc, copper, cadmium, and lead concentrations among the study sites were 5 to 812 μg/L, less than 0.12 to 5.2 μg/L, less than 0.0026 to 4.9 μg/L, and 0.1 to 18.6 μg/L, respectively. The abundance of several populations and community metrics showed a significant negative response to heavy metal pollution. Mayfly diversity and abundance was relatively sensitive to heavy metal pollution. In addition, the biomass of groups of macroinvertebrate taxa that are highly available for salmonids were significantly reduced at metal-polluted sites; this decrease in the most highly available group was noticeable (99% at the heavily polluted upper sites and 69% at the moderately polluted lower sites in spring). These results suggest that we should consider the indirect effect of pollution on food availability for the conservation of fish populations that depend on drifting macroinvertebrates.