The benthic ecosystem has been greatly altered by environmental pressure over the past several decades. Compared to some well-studied large bays, the situation in populated small bay areas is still under-investigated. In this study, 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. We found that ostracod abundance and diversity exhibited an inner-outer gradient in Deep Bay, shaped by eutrophication and pollution from human activities. Faunal composition was also characterized by inner-outer difference, as well as difference between Hong Kong and Shenzhen areas, whereby Hong Kong was more influenced by eutrophication, and Shenzhen was more affected by metal pollution. Ostracod distribution and their environmental preference in Deep Bay were consistent with broader studies in Hong Kong, strongly supporting the idea that ostracods are a useful bioindicator of coastal benthic ecosystems. Our study emphasizes the importance of studying an uncomplicated system with fine-scale sampling, as this approach offers a clear and direct understanding of how benthic ecosystems are shaped by distinct coastal environmental problems.