Detailed study of Oxfordian coral-microbialite reefs in the Swiss Jura Mountains has identified major paleoecological variations in space and time, which are attributed to environmental changes. Micro- and macroscale semi-quantitative analyses of microbialite types, micro-encrusters, bioerosion, corals, and other macrofauna composing the reefal facies were performed. Three main trophic structures (dominant nutritional modes) were recognized: phototrophic-dominated, balanced photo-heterotrophic, and heterotrophic-dominated. A phototrophic (light-dependant) fauna dominated reefs growing in pure carbonate and nutrient- poor environments, where sedimentation rate was the main factor controlling reef growth. In mixed siliciclastic-carbonate platform environments, a balanced photo-heterotrophic fauna with periodical shifts to heterotrophic-dominated associations was induced by freshwater and sediment run-off into closed, shallow lagoons. In this case, the main factors controlling reef growth were the distribution and accumulation of terrigenous sediment on the platform and/or associated nutrient availability. The balanced photo-heterotrophic structure found in mixed carbonate-siliciclastic settings produced the most diversified reefs, suggesting that these Oxfordian reefs preferentially thrived in water moderately charged with nutrients (mesotrophic environment). In the case of strong siliciclastic accumulation and/or strong increase in nutrient availability, coral reef diversity dropped drastically and heterotrophs dominated the trophic structure. A model of the evolution of trophic structure in these reefs as a function of the governing environmental factors is proposed. Focusing on the dominant nutritional mode at each step in reef evolution allows a detailed characterization of reefal structure and a better understanding of the processes leading to coral reef settlement, development, and demise.