The estuaries of Tampa Bay, Sarasota Bay, Lemon Bay, and Upper Charlotte Harbor are contiguous waterbodies located within the subtropical environment of Southwest Florida. Based on an examination of rainfall data over the period of record (1916-2001) within the watersheds of these estuaries, there is no evidence for spatial differences (at the watershed level) or monotonic trends in annual rainfall. During the 1980s, nitrogen loads into Tampa Bay and Sarasota Bay (generated primarily by domestic wastewater treatment facilities) were reduced by 57% and 46%, respectively. In response, both Tampa Bay and Sarasota Bay have lower phytoplankton concentrations, greater water clarity and more extensive seagrass coverage in 2002 than in the early 1980s. As there is no evidence of a concurrent trend in rainfall during the period of 1982-2001, it is unlikely that variation in rainfall can account for the observed increase in seagrass coverage in these two bays. In contrast, seagrass coverage has remained relatively constant since the mid 1980s in Lemon Bay and Charlotte Harbor. Domestic wastewater treatment facilities are minor sources of nitrogen to Lemon Bay, and water clarity in Charlotte Harbor varies mostly as a function of dissolved organic matter and non-chlorophyll associated turbidity, not phytoplankton levels. Even in estuaries that share boundaries and are within 100 km of each other, varied responses to anthropogenic changes and natural phenomena were observed in water quality and associated seagrass extent. Resource management strategies must take into account system-specific factors-not all strategies will result in similar results in different systems.