Predatory fishes often have strong top-down effects on coastal marine ecosystems and are considered a priority for conservation and management. Predator activity can influence prey distribution, abundance, and foraging behaviors, and is likely to influence habitat by impacting ecological and environmental characteristics as well as presence of competitor species. There are knowledge gaps of the effects of functional diversity, non-consumptive predator association, and environmental effects on fish assemblages, particularly within the Greater Caribbean region. In this study, effects of apex marine predatory fishes on diversity and abundance of prey ichthyofaunal communities were examined in putative predation low-risk (north side = lagoon) and high-risk (south side = flat) areas around South Bimini Island, The Bahamas. Baited remote underwater video surveys (BRUVs, n = 100 sites) deployed in the two nearshore habitat types captured abundance and potential predator-prey interactions, which were compared to assess potential risk effects within low-risk and high-risk habitats. Results showed a difference in ichthyofaunal communities between the two habitats, with teleost abundance highest on the south side. Depth, temperature, salinity, and dissolved oxygen were significantly linked to biotic assemblages. There were no differences in flight (escape) behavior of prey from predator (sharks versus great barracuda), suggesting that predator avoidance was a minimal factor in ichthyofaunal community structures. In the rapidly developing Greater Caribbean region, knowledge of ichthyofaunal communities and predator-prey interactions in different coastal habitats can better inform management regarding ecological changes over time and between island locations.