As coral reef habitat quality degrades globally due to the increasing severity and frequency of environmental stressors, the diversity and abundance of reef organisms change in response. These shifts can have profound impacts on ecosystem service provision. The unprecedented nature of climate-driven disturbances limits our ability to predict the future of coral reefs based on historical benchmarks. This work explores the dynamic relationship between reef structural complexity, fish assemblage structure, and ecosystem service provision using the MizerReef R package, a new tool that leverages size spectra theory in a coral reef context. Model predictions agree with empirical observations, indicating that the trait composition of coral reef fish assemblages changes significantly in response to changes in habitat structure. Results suggest that herbivores broadly benefit from increased structural complexity in any form. At the same time, small-scale structures may limit the productivity of large piscivores, highlighting the potential trade-offs for fisheries in areas with abundant small-scale structures such as branching coral thickets. The MizerReef package offers a valuable addition to the ecosystem management toolbox as we attempt to preserve the crucial services coral reefs provide.