Harbours with limited water exchange are hotspots of contaminant accumulation. Antifouling paints (AF) contribute to this accumulation by leaching biocides that may affect non-target species. In several leisure boat harbours and reference areas in the Baltic Sea, chronic exposure effects were evaluated using caging experiments with the snail Theodoxus fluviatilis. We analysed variations in ecologically relevant endpoints (mortality, growth and reproduction) in concert with variation in metallothionein-like proteins (MTLP) levels. The latter is a biomarker of exposure to metals, such as copper (Cu) and zinc (Zn), which are used in AF paints as active ingredient and stabilizer, respectively. In addition, environmental samples (water, sediment) were analysed for metal (Cu and Zn) and nutrient (total phosphorous and nitrogen) concentrations. All life-history endpoints were negatively affected by the exposure, with higher mortality, reduced growth and lower fecundity in the harbours compared to the reference sites. Metal concentrations were the key explanatory variables for all observed adverse effects, suggesting that metal-driven toxicity, which is likely to stem from AF paints, is a source of anthropogenic stress for biota in the harbours.