We investigated the abundance, diversity, composition, and distribution of ostracods (a meiobenthic group) and their interactions with eutrophication and pollution through high-resolution sampling of surface sediment in Deep Bay, a small semi-enclosed riverine bay adjacent to two of the world’s most populated cities: Hong Kong and Shenzhen. The results support the idea that ostracods are a useful bioindicator of coastal benthic ecosystems shaped by distinct environmental problems.