Coral reefs worldwide are suffering degradation from increasing fishing pressure, pollution, diseases, and coral bleaching. One important ecological consequence of such degradation is an increase in biological erosion, or bioerosion, of the coral framework by boring and grazing organisms. Therefore, it has become essential to understand the factors that control the processes and agents of bioerosion. The aim of my dissertation is to understand how organic and inorganic nutrients and herbivory affect the bioerosion of carbonate substrates by microbial endolithic organisms (bacteria, fungi and algae), an often overlooked component of bioerosion processes in coral reefs. Results of controlled experiments using herbivore-exclusion cages and fertilizers at Glovers Reef, Belize consistently showed significant effect of nutrients in stimulating microbial endoliths' substrate colonization and bioerosion rates of Strombus gigas shells. The addition of inorganic nutrients increased bioerosion rates by a factor of 8 to 15 in comparison to control treatments. Changes in nutrient ratios changed microbial endolithic community structure. The addition of nitrogen alone or in combination with phosphorus stimulated green algae, the addition of phosphorus alone stimulated cyanobacteria, and the addition of organic matter alone stimulated fungi. The inclusion of herbivores reduced observed bioerosion rates by half, demonstrating the importance of herbivory in modifying bioerosion processes. Field experiments on the relationship between water quality and the amount of microbioerosion in Lambis chiragra shells in nine coral reefs in East Africa demonstrated that other factors within reefs may interact with nutrients in determining bioerosion rates. Results suggested that epilithic algal cover, particularly crustose coralline algae, may decrease microborer colonization and bioerosion rates by reducing light conditions within substrates, so that no direct effects of nutrients on bioerosion rates are detected. A critical review of the evidence for nutrients as a primary control of bioerosion by different bioeroder groups (microborers, macroborers, and grazers) suggests that macroborer abundances reflect increases in nutrient conditions and may therefore represent a useful indicator of eutrophication and coral reef "health". This dissertation contributes to a better understanding of the factors affecting bioerosion by microbial endolithic organisms, which are important but often overlooked agents of bioerosion in coral reefs.