The importance of the El Niño-Southern Oscillation (ENSO) on regional-scale climate variability is well recognized, although the associated effects on local weather patterns are poorly understood. Little work has addressed the ancillary impacts of climate variability at the community level, which require analysis at a local scale. In coastal communities water quality and public health effects are of particular interest. Here we describe the historical influence of ENSO events on coastal water quality in Tampa Bay, Florida (USA) as a test case. Using approximate randomized statistics, we show significant ENSO influences on water quality, particularly during winter months, with significantly greater fecal pollution levels during strong El Niño winters and significantly lower levels during strong La Niña winters as compared to neutral conditions. Similar significant patterns were also noted for El Niño and La Niña fall periods. The success of the analyses demonstrates the feasibility of assessing local effects associated with large-scale climate variability. It also highlights the possibility of using ENSO forecasts to predict periods of poor coastal water quality in urban regions which local agencies may use to make appropriate preparations.