Warniak is a shallow eutrophic pond-type lake, part of the Mazurian Great Lakes. Since the late 1960s it has been subject to long-term experiments: introducing fish stocks of varied size and composition, resulting in massive physical, chemical and biotic changes in the lake’s ecosystem. The aim of this study was an assessment of changes in the lake’s mollusc assemblages 17 years after the first investigations (1998). The comparison of malacofauna in 1998 and 2015 showed changes in its composition, a significant decline in species richness and abundance, reduction in vertical distribution, increase in spatial variation of composition, richness and abundance. The proportion of rare species (i.e. found in one or two samples) increased from 17.4% to 64.7%. The dominance pattern became simplified and the frequencies of most species decreased. In 2015 Anodonta cygnea (L.) was still the most widespread unionid and one of the three most frequent species. The changes in the malacofauna occurred despite the lack of significant changes in the lake trophy. The deterioration of conditions for molluscs may result mainly from the impoverishment of macrophytes and the decrease in their abundance.