Thirty surface sediment samples were collected from the Pearl River Estuary, South China, and benthic foraminifera were analyzed in order to understand the relationship between foraminiferal assemblages and environmental parameters. Multivariate analyses showed that the foraminferal assemblages (i.e., abundance and diversity) are correlated with the hydro-sedimentary gradients within the estuary. In addition, the dominant faunal composition seems to be largely influenced by food availability and trace metal contamination in surface sediments. A comparison with historical data from 1980s demonstrated that the foraminiferal abundance and diversity in the lower estuary have dramatically decreased over the last three decades, together with a significant shift in the dominant species. This is most likely due to the cumulative impacts of eutrophication and Cu contamination caused by human activities in the Pearl River basin. This work confirms the value of benthic foraminifera as bio-indicators in polluted estuarine environments.