Fish community composition and functional diversity is determined by biophysical factors and habitat structure.

Reef fishes maintain many key ecological functions and services for coral reefs. Interactions with their environment have the potential to mediate their distribution, habitat use, and contribution to ecological processes. However, rising anthropogenic pressures and climate change have begun to alter reef environments, modify reef architecture, and disrupt food web dynamics through targeted fishing practices. We examined the impact of habitat structure (rugosity and fractal dimension), biophysical conditions (coral cover, depth, temperature, chlorophyll-a, and wave exposure), and anthropogenic pressures (effluent pollution, fishing pressure, and nearshore development) on biomass, species richness and ecological function in terms of functional diversity and trait-based composition of reef fish communities. Across 89 coral reef sites, we captured fine-resolution Structure-from-Motion photogrammetry and conducted stationary point count surveys to record fish populations. Habitat structure emerged as the primary driver of reef fish biomass, species richness, functional richness, and functional divergence, though biophysical factors also played a role. Traits of reef fish, including diet, grouping behavior, and position in the water column, were all largely influenced by habitat structure in ways that aligned with expectations when considering habitat preferences, foraging behaviors, and predator-prey dynamics. We predicted populations across different reef regimes, characterized by high and/or low values of rugosity, fractal dimension, and coral cover, and found that degraded reefs will support smaller communities with limited traits, which will likely translate to losses of ecosystem functions and services. We highlight the main factors influencing species diversity, trophic structure, and the complexities of ecological communities. Our findings suggest that habitat structure in tandem with well-known biophysical factors can provide insight into reef fish community patterns and should be prioritized as additional metrics when monitoring reef fish populations across space and time.