The coral reefs of Kane'ohe Bay, on the windward coast of O'ahu, Hawai'i, have changed markedly over the last half century. Some of the most spectacular coral reefs in Hawai'i were reported from Kane'ohe Bay in the late 1800's and early 1900's, but with the beginning of extensive military dredge and fill operations during the World War IT era, conditions in the bay began to change dramatically. After the War, rapid urbanization of the area began and conditions in the bay continued to decline until pressure from the public and scientific community led to the diversion of the large sewage discharges in the southeast lagoon to a newly built deep ocean outfall outside the bay in 1977-1978. Although conditions temporally improved, recent surveys indicate that current conditions in the bay are not as favorable as expected. This study provides a time series analysis of changes in coral and algae cover in Kane'ohe Bay based upon a series of coral reef surveys conducted throughout the bay in 1970171, 1983, and 1990. Beginning in 1970171, conditions in the bay were highly degraded and scientists speculated that eutrophication and sedimentation, as a result of urbanization and construction, were the primary cause of an observed decline in lagoon corals communities in the southeast lagoon and an explosive growth of the green "bubble algae", Dictyosphaeria cavemosa, which was smothering corals in the middle lagoon. In . 1983, six years after major sewage discharges were diverted from the bay, surveys indicated dramatic improvements in water quality and the reefs showed signs of recovery. D. cavemosa algae levels, associated with earlier nutrient pollution, plummeted to less than twenty percent of their former abundance levels and coral cover increased by over two hundred percent. Although it was predicted that the coral reefs of Kane'ohe Bay would continue to recover, surveys in 1990 indicate that coral recovery slowed or ceased and the growth of the green "bubble algae", D. cavemosa, more than doubled compared to 1983 levels. In addition to the failure of the t~o dominant coral species Porites compressa and Montipora capitata to continue to recover, almost all of the less common coral species including Pocillopora damicomis, Fungia scutaria, Cyphastrea ocellina, and some others, showed significant declines in reef cover. Although this study was not able to detennine the exact causes of the observed changes in Kane'ohe Bay, it is suggested that high nutrient inputs provided favorable conditions for the changes in coral and algae cover. High nutrient levels are thought to have been derived from a number of sources including chronic sewage pollution, increased sedimentation from runoff, and reef kills associated with acute but large episodes of freshwater runoff. Some of these nutrient inputs may have been the result of non-point source and point source sewage pollution derived from leaky sewer lines, cesspool and septic tank discharges, commercial tour and recreational boat waste discharges, and periodic sewage bypasses from municipal wastewater treatment plants and sewage pump stations. Other nutrients may have been derived from increased sedimentation following extensive land clearance, land development, and highway construction. Additional factors may include a decrease in herbivorous fish species owing to over fishing and the ability of D. cavemosa algae to concentrate nutrients from underlying substrates and excretion from infaunal organisms. Other factors such as increased nutrient recycling from the sediments, possible increased nitrogen fixation from reefs, and natural fluctuations in relative species abundances may also be responsible for some of the observed changes in coral reef community structure. Although rare, the largest nutrient fluxes followed the catastrophic freshwater reef-kill events caused by severe rainstorms in conjunction with low tides and low wind conditions in 1965 and 1987-1988. Although the cause and effect relationship is still uncertain, the highest levels of Dictyosphaeria cavemosa algae ever recorded in Kane'ohe Bay occurred in the years following these storm events. Results of this study indicate that further research is needed to monitor ongoing conditions in the bay and determine what is preventing the reef ecosystem from returning to its former more pristine condition. Because water quality parameters generally remained the same or improved compared to previous polluted conditions, it is suggested that current measures of water quality are not reliable in forewarning against coral reef degradation in Kane'ohe Bay. Although a reduction in all future development in and around the bay would probably help maintain environmental conditions at the status quo, additional regulations and enforcement may be needed to help reduce disturbances caused by existing land and water use. It is suggested that a reduction in nutrient inputs to the bay would be beneficial to reef corals. Recommendations made by the Kane'ohe Bay Task Force outlined in the Kane'ohe Bay Master Plan should serve as a model and be implemented as soon as possible. Continuing assessment of the Kane'ohe Bay coral reef ecosystem and surrounding watershed will then need to be made on a regular basis to ensure that further degradation of the reefs is not occurring. / Thesis (M. A.)--University of Hawaii at Manoa, 1995. Includes bibliographical references (leaves 166-175).