This study delves into the diverse marine habitats of Jubilee Shoals, a submerged rocky reef off Pissouri Bay, Cyprus (eastern Mediterranean). The habitats include Posidonia oceanica meadows on the plateau, coralline communities on the vertical walls, and a cave system at its base. Utilizing closed-circuit rebreathers, trained cave divers quantitatively described the epibenthic communities and biodiversity within the cave system, ensuring both safety and high-quality data collection. Rebreathers allowed silent, bubble-less operation, efficient gas usage, extended dive times, reduced decompression times essential for detailed observation. The findings underscore the need for rebreathers in scientific exploration of deep-water environments, emphasizing their advantages. This approach facilitates undisturbed marine life observation and minimizes environmental impact, paving the way for future research and conservation in similar ecosystems.