The effects of both point and non-point sources of pollution on coral reef ecosystems in Mamala Bay were studied at three levels of biological organization; the cell, the population and the community. The results show a uniform lack of negative environmental impact. Calcification and growth show no relation to point or non-point sources of pollution within the bay. Neither do species abundance patterns, diversity or community structure. Changes in water quality caused by rainfall and wave events are too small and too short lived to affect coral reef ecosystems in the bay. Species abundance patterns and community structure of coral ecosystems in the bay appear to be related to the effects of large hurricane wave events in 1982 (Iwa) and 1992 (Iniki). Recovery of coral reef ecosystems in Mamala Bay is now taking place from damage sustained during and after these storms, and from an earlier period of severe environmental degradation prior to 1977 when raw sewage was discharged into the bay at 13 m depth off Sand Island. Not withstanding future disturbances, existing sources of point and non-point source pollution are not expected to interfere with the recovery process now ongoing in Mamala Bay, and long-term biological processes should eventually return the coral ecosystem to a more mature successional stage. This data set includes surveys from 16 stations in Mamala Bay with comparisons to Hanauma Bay and Sunset Beach. Coral data types include percent coral cover, calcification rates of P. Lobata, bioerosion of P. Lobata, and coral species diversity. The data also includes water quality parameters for control periods, after wave events, and after rain events. Finally, data from sediment traps are given.