Mining is a relatively highly monitored industry. While chemical pollutants (toxic ions, radionuclides, etc.) have mostly been eliminated from mining waters, other types of environmental pollution (temperature regime alterations, high concentrations of various anions, etc.) can affect benthic invertebrates. In this study, we focused on the effect of mining water effluent on the diversity and density of aquatic Clitellata. Four sampling sites were selected. Three sites in a natural stream (the Nedvědička River, Czech Republic), one upstream and two downstream from the mining effluent, and one site on the mining waters were sampled monthly during 2008–2009. Environmental variables were recorded in and samples were collected from two types of habitats — riffles and pools. The response of clitellate assemblages was evaluated using principal component analysis and generalised estimating equations. The results indicated that the mining effluent caused partial species exchange and had negative effects on clitellate taxa richness and abundance. These responses were specific to both the habitat (riffle/pool) and species sampled. In each of the different taxa studied, we observed one of four typical clitellate responses: (a) elimination of stenotherm species; (b) reduction of clitellate species followed by quick recovery; (c) neutral response; or (d) positive influence. We found that aquatic clitellates, which are considered to be eurytopic with broad ecological valences, are also sensitive to even slight environmental pollution.