Coral reefs are experiencing an increase in seawater temperature and eutrophication due to the effects of climate change and anthropogenic stressors. This has resulted in a regime shift from coral-dominated systems to algae and/or sponges-dominated systems. So far, most research has focused on the ecological responses of specific groups and over short time scales, while there is scarce information about the adaptive potential of whole communities. To understand how species communities’ assemblages will develop under current environmental changes, it is important to understand the geological cycles and the settings under which the current marine communities have risen. We will use the clearly defined spatial-temporal context of marine lakes as natural mesocosms to study the trajectories and responses of marine communities to environmental change. By selecting lakes and open water reefs that represent a gradient in water temperature and nutrient levels, we will study the current and historical diversity patterns and their interaction with different environments. This project will inquire on the adaptive community response to environmental change over ecological and micro-evolutionary timescales through traditional underwater surveys, 3D models, the analysis of sediment cores, and environmental DNA.