The coral reefs of Bonaire have been reported to be one of the most pristine reefs, with the reefs on the leeward coast of Bonaire regarded as one of the healthiest reefs of the Caribbean (NOAA 2008; Sommer et al. 2011; Jackson et al. 2014). Nonetheless, Bonaire is a growing popular tourist destination and the reefs have been increasingly exposed to anthropogenic stress in addition to natural disturbances. The overarching question of this project addressed the large and small-scale variation in benthic and fish communities of the reefs on the leeward side of Bonaire. However, this report focuses on describing the fish communities of these reefs, and looks into the effect of benthic community composition on fish community assemblages. Our fieldwork set-up allowed us to look into large scale differences (between zones), and small-scale differences (between sites, within zones). Additionally, since fish observations were done on the same transect as benthic measurements, with this set-up, we were also able to look into the effects of benthic composition on fish community composition. To visualize trends in species biomass composition we did a cluster analysis and plotted the clusters in a non-metric multidimensional scaling (nMDS). To see which benthic categories had an effect on fish composition, we plotted an environmental fit (Envfit at P < 0.05) with benthic categories. Also, to check the effect of site location, the clusters are plotted on a Bonaire map. We report clear differences in fish species richness, diversity and biomass between the two zones, with the deeper zone showing greater numbers. There was greater variation in both fish and benthic communities in the lower-terrace (the shallower zone), and this variation reflected the degradation gradient along the leeward coast of Bonaire. Sites located around the busy tourist center showed a trend towards lower fish biomass and richness, lower coral cover and diversity, and lower topographic complexity. Whereas sites in the same zone (same depth) located within the marine park, a protected area, scored highest in the same categories. The drop-off, a deeper zone, showed far less variation in all categories. From these results it can be concluded that effects of habitat degradation on benthic communities reflect on fish communities, especially in shallower zones. Our results also demonstrate that protected areas have a positive effect on benthic and fish communities, reiterating the importance of these areas. The inclusion of Bonaire fishery data would provide an interesting insight and would clarify even more the variation found across sites.