Most coral reefs in the wider Caribbean have been showing alarming signs of decline in recent years. Coral diseases and bleaching were monitored seasonally from 2003 to 2007 using the modified CARICOMP protocol with a stratified design to assess spatial and temporal variability in community level coral disease prevalence (proportion of affected colonies) at six reefs along an inshore-offshore gradient in La Parguera, southwest coast of Puerto Rico. Temperature loggers were deployed in each reef to assess co-variation between disease prevalence and virulence, and temperature. Virulence was assessed in Montastraea faveolata by tagging colonies, marking diseased edges, photographing and following them through time. Overall, all major reef-building species and other common reef groups were variously affected by disease and bleaching. Eleven diseases affected up to 42 species of scleractinian corals, 5 octocorals, 2 hydrocorals, 3 zoanthids, 2 sponges and 2 crustose coralline algae. Bleaching affected 52 species of corals, 22 octocorals, 3 hydrocorals, 2 zoanthids and 3 sponges. The prevalence of the diseases compromised coral health and varied significantly between seasons within years as well as among reefs within years and across years for each reef. White plague, yellow band and bleaching were the most prevalent and damaging diseases. Three white plague, two yellow band outbreaks and three bleaching events of different intensities were observed during the five years of study. Yellow band disease increased in prevalence (from 4 % to 30%) and virulence (0.8 ± 0.2 to 3.9 ± 1.4 cm/month) over 6 years, becoming one of the most important agents of coral mortality. Higher disease prevalence was consistently found at the mid-shelf and shelf-edge reefs than in reefs closest to the shoreline. The combination of white plague disease outbreaks, the intensive bleaching of 2005 and the chronic yellow band caused an average 53 % of live coral tissue loss in four years, the highest coral mortalities ever recorded in southwest Puerto Rico.