The Caribbean is well known for its tropical islands fringed by beautiful coral reefs. However, reefs nowadays shift from coral dominance to dominance by algae and cyanobacteria, probably due to eutrophication and overfishing. This is known for shallow reefs on the leeward side of islands. The deep (mesophotic, > 30 m deep) reefs are considered to be important as providers of offspring to shallow reef communities that are arguably more affected by climate change, overfishing and unsustainable coastal development. Mesophotic reefs are probably also important on the wind ward side of islands: due to high wave exposure benthic communities are largely confined to the mesophotic region. These mesophotic reefs are still mostly unexplored because of their remoteness or inaccessibility. Incidental deep dives and submarine dives have established sites where well developed reef communities have been found (Curaçao), but also where large areas with cyanobacterial mats (Bonaire) were observed. Cyanobacteria are known to proliferate under eutrophied conditions and to be stimulated by global warming. We hypothesize that submarine groundwater discharge (SGD) is a main and continuous nutrient transport route from land to sea on Caribbean islands and cause proliferation of cyanobacterial mats. Understanding its role in the onshore-offshore hydro(geo)logy of the island is a prerequisite for cost-effective waste (water) management on the island and consequently improved health of the coral reefs.