The impact of pollution on the trophic ecology of the Kelian River (Borneo, Indonesia) was studied by comparing food webs (on the basis of gut analysis and field and laboratory observations) at six sites. The upper sites were in pristine rainforest but the river became increasingly polluted downstream, largely owing to sedimentation from alluvial gold mining activities. Four previous studies all showed a downstream decrease in macroinvertebrates (mean abundance: 272 per 400 cm2 at Site 1 dropped to 2.6 at Site 6; mean number of taxa: 37.6 at Site 1 down to 1.6 at Site 6), and this was highly correlated with suspended solids. Food webs also reflected the effect of pollution. Cleaner sites had more complex food webs, with more elements, links, higher linkage density and higher complexity than did downstream polluted sites, which lacked grazers, shredders and filterers. Several taxa that were grazers at clean sites became collector-gatherers at polluted sites. Despite the enormous impact of pollution, cessation of alluvial mining activities resulted in some recovery. The resilience of the fauna is likely to be enhanced by the tropical conditions with high rainfall, rapid flow rates and high temperatures, coupled with rapid life cycles. Fish distribution and diets did not appear to be affected by pollution.