Rising sea temperature and decreasing water quality alter the look and function of tropical coral reefs. Heat and high nutrient loads cause coral-dominated reefs to shift towards communities dominated by algae, sponges, and benthic cyanobacterial mats (BCMs). These shifts in benthic community composition lead to reorganization of food webs and species interactions which alters ecosystem functioning. To predict the responses of coral reefs to the environmental and anthropogenic stressors of high sea temperatures and nutrient loads, we study ecosystem functioning in marginal reef communities along a gradient of water temperatures and nutrient levels. Marine lakes found in Raja Ampat, Indonesia, are natural analogues for future climate change scenarios where marginal reef communities live in eutrophic islands of sea water, forming a gradient in sea temperature. These communities will be compared to open sea reef communities along a gradient of nutrient levels. First, trophic interactions of organic matter transfer between the major functional benthic groups (coral, macro algae, sponges, turf algae, and BCMs) are quantified through pulse-chase aquarium experiments using labelled stable isotopes of carbon and nitrogen. Second, metabolic functioning of those benthic groups is evaluated with in situ incubations along the environmental gradients. Metabolic fluxes, such as photosynthesis, respiration, organic matter production and consumption will be quantified. Third, relative growth rates and spatially competitive interactions of the benthic groups are recorded on 2D-photographed transects and 3D-modelled permanent quadrants. Last, food web structure is compared among benthic communities along the environmental gradients through stable isotope analysis.