Human activities cause rapid eutrophication and increased water turbidity in aquatic ecosystems, but their effects on fish communication and colour signals remain of debate. In particular, melanin-based coloration in fish has been understudied, because it was believed to be less costly to display than carotenoid-based colours. Here, we measured the phenotypic divergence of melanin-based coloration in 17 populations of gudgeon (Gobio occitaniae) along a turbidity gradient. We also tested the short-term plasticity of coloration using a reciprocal transplant experiment. We found strong variability in melanin-based coloration along the turbidity gradient: interpopulation divergence in coloration was higher than predicted by genetic drift, and fish were paler with increasing levels of turbidity. Finally, a reciprocal transplant experiment revealed that fish transplanted into more turbid habitats expressed a paler melanin-based coloration, suggesting that melanin-based coloration was highly plastic in the short term. Overall, our results suggest that eutrophication in human-altered rivers can rapidly alter melanin-based coloration, with potential consequences for fish visual communication and sexual selection.