We used microsatellite DNA markers to examine the impact of the Fundão Dam failure, one of the world’s worst mining-related environmental disasters, on the genetic diversity of four marine and estuarine fishes across the Brazilian east coast's continental shelf and estuarine ecosystems. The strong mud flow along the Doce River and nearby areas resulted in changes in genetic diversity, with all species exhibiting low genetic diversity indices, primarily in estuarine species, and particularly those with a greater association with the substrate. Furthermore, the low M-ratio values in all species tested indicated a recent decrease in the effective population size. Estuarine species, particularly the slipper sole Trinectes paulistanus, were more directly impacted by the mud plume than marine species. The loss of genetic variability due to population decline is concerning because it is ultimately an important component in determining the ability of marine fishes to adapt to environmental changes. Combining genetic data from four fish species with different behaviours, habitats, life histories, and economic values revealed that genetic diversity was a valuable tool for assessing the effects of the Fundão Dam failure.