The coral reefs of Bonaire, providing resources and environmental services, are often ranked among the richest, most resilient and least degraded in the Caribbean, but they are not escaping the global degrading trend in coral reefs. Identifying and combatting local stressors, increases the resilience to global stressors. Research has shown that even the deeper, relatively unexplored reefs, mesophotic coral ecosystems (MCE), ranging from 30 to 150m in depth, are being impacted by anthropogenic disturbances. As the MCEs start where Scuba diving stops, and submersibles are often too costly, this study deployed an ROV to explore and monitor the shallow (5-20m) and the upper-mesophotic (40-60m) reefs at eight sites along the leeward coast of Bonaire. These sites were subdivided into different zones, showing a gradient in human impact and water quality. The imagery obtained by the ROV is of adequate quality, allowing for identification to genus level if not species level, and showed comparable results in estimated percentage coral cover with other recent studies. The benthic community composition changed along the vertical (depth) and horizontal (human impact and water quality) gradient. Benthic cyanobacterial mats were found around 40-60m depth, covering large parts of the ocean floor. Hard and soft corals, sponges, macroalgae and crustose coralline algae occurred at 40m depth at six of the eight monitored sites, indicating the presence of MCEs, and only at one site (Karpata), hard corals were present at 60m depth. Coral cover showed a clear increasing trend with decreasing human impact, addressing the need for a better understanding of heterogeneity among sites and local conservation measures. Developments in underwater robotics and machine learning enable more research on these hidden coral reefs and identification of the effect of local stressors on MCEs.