Simple SummaryMayflies (Ephemeroptera), stoneflies (Plecoptera), and caddisflies (Trichoptera) (EPT) are aquatic insects that are well known to the general public and are commonly used as indicators of environmental quality in water management. Knowledge of how EPT communities react to human-induced gradients in real environments can be important, for example, during the assessment of the implications of newly planned or currently active human disturbances for natural or cultural landscapes. We sampled a stream ecosystem affected by mining and smelting industries and communal wastewaters with pronounced concentrations of cadmium, lead, and zinc, as well as high levels of pesticides, pharmaceuticals, illegal drugs, and sewage-derived organic matter. Changes in other environmental factors such as increases in temperature were also studied at the affected sites. The abundance and species richness of stoneflies fell rapidly at the study sites. The richness of mayfly families also declined, from four to one, even though overall mayfly abundance was not affected. Conversely, the abundances of caddisflies were higher at the affected sites, and their richness did not decrease. This study will provide feedback for ecotoxicologists who perform better controlled and manipulated tests in laboratories, although any such test results are limited by simple artificial environments.Abundances of EPT larvae sampled in a Central European locality affected by mining and smelting, as well as by the continual inflow of treated communal wastewaters (WWs), were recorded. High concentrations of trace metals in water (maximum 1200 µg·L–1 for zinc) and sediments (maximum 140,000 mg·kg–1 in dry weight for lead) were found at the most contaminated sites. The highest loads of pesticides, pharmaceuticals, and illegal drugs were found under the WW effluent. Other associated factors such as the physicochemical parameters of the water and alterations to microhabitats were also evaluated and taken into account. Although EPT richness was lower at affected sites, abundances did not fall. Stoneflies were dominant at unaffected sites, while caddisflies dominated at affected sites. Only baetid mayflies were detected at the sites contaminated by trace metals and WWs; ephemerellid, heptageniid, and leptophlebiid mayflies were absent from these sites. The site contaminated by trace metals was also inhabited by numerous limnephilid caddisflies, in which limb malformations were detected in up to 11.8% of all specimens of a single taxon. Downstream from the entrance of the WWs, the locality was dominated by hydropsychid caddisflies. The increasing prevalence of predator or passive filter-feeding strategies in these EPT communities was significantly related to increasing water conductivity and acute ecosystemic exposure to ‘poorly treated’ WWs.