The Florida Keys reef tract has transitioned from a complex, hard coral-dominated ecosystem to a less structured, soft coral-dominated one, largely due to changing climates and anthropogenic stressors such as fishing and marine debris. These artificial structures are becoming crucial habitats for understudied marine taxa known as cryptofauna. With the degradation of coral reefs, the fate of these organisms remains uncertain. In response, the SCUBA diving community has initiated marine debris removal efforts to clean the seafloor, though the interactions between debris and marine species complicate these efforts. This study employed a four-step approach to examine these interactions and assess the effects of debris removal on marine organisms. First, a benthic cover census was conducted at 30 reefs in the middle Florida Keys to analyze substrate and debris composition. Next, mobile cryptofauna communities were studied to compare populations on natural structures versus those on marine debris using Autonomous Reef Monitoring Systems (ARMS) on 14 patch reefs. The third step used a mixed-methods approach to evaluate how human factors influence debris removal decisions among divers. Finally, the study assessed the physical impact of debris removal by measuring the diversity and biomass of displaced marine taxa for 18 dive removal events. These findings underscore the need for more detailed awareness regarding marine debris impacts and removal on coral ecosystems, emphasizing that understanding the role of marine debris serves as novel structure and habitat is vital for overall reef health and management.