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Hydrodynamic processes are important in all marine environments and on coral reefs drive patterns of habitat zonation, community structure, and biodiversity. Abrupt geomorphological features like pinnacles and seamounts often possess distinct localized currents and these habitats are also often characterized by high abundance and biomass of fishes. However, differences in fish community structure between pinnacles and emergent reefs, and their key drivers are poorly understood. In this study, we compared fish communities among emergent fringing and offshore coral reefs, and submerged pinnacle reefs in Papua New Guinea. Submerged pinnacles possessed higher fish biomass, abundance, and species richness than both fringing and offshore emergent reefs. We collected in‐situ current speed and temperature data over a full year at each reef and used random forest analysis to investigate the relative influence of hydrodynamics compared to other well‐established drivers of reef fish biodiversity, including habitat and biogeographic factors. Environmental variables explained 70%, 52%, and 5% of variability in models for species richness, abundance and biomass respectively. In all models, average current speed, current speed variability, and reef area were consistently among the most influential variables. Models examining relationships between fish biodiversity metrics and current speed did not yield conclusive results but did highlight the association of distinct hydrodynamic regimes on pinnacles with high fish richness, abundance, and biomass. Our study highlights the strong influence of reef‐scale hydrodynamics on fish biodiversity and demonstrates the ecological value of small, submerged coral reefs, which are globally numerous yet remain understudied in coral reef ecology. [ABSTRACT FROM AUTHOR]