Contaminated beaches are a public health and economic concern among coastal regions. The concentration of fecal indicator bacteria (FIB) such as enterococci, fecal coliforms and total coliforms, have often been used to assess the potential public health risk at local beaches including Imperial Beach located in San Diego County, California. Various sources contribute to the microbial load along the coastline to include: the treatment and disposal of disinfected wastewater and run off from shore or nearby rivers. These sources ability to contaminate the shoreline may increase during a phenomenon known as the El Niño—Southern Oscillation, an irregular periodical variation in winds and sea surface temperatures over the tropical eastern Pacific Ocean. The primary goal of this study was to elucidate how this ENSO phenomenon impacts FIB levels at the Imperial Beach, CA shoreline, and secondly to assess whether the South Bay Ocean Outfall (SBOO) and or the Tijuana river significantly contributes to an increase in shoreline fecal contamination in conjunction with ENSO events. Spearman correlations between the fecal densities of respective ENSO events and both sea surface temperature (SST) and rainfall were conducted at the Imperial Beach Shoreline and the South Bay Ocean outfall. For both locations, FIB vs. SST's showed no statistical significance while a correlation was found between FIB vs. rainfall (p < 0.05). Seasonal analysis using Kruskal-Wallis and Dunn's test showed a statistical difference between El Niño, La Niña and neutral years median FIB levels (p < 0.05); total coliforms for winter, enterococci for spring, all FIB's in the summer, and total coliform and enterococci for fall; with El Niño years being the highest for all seasons. Cluster analysis of FIB concentrations at Imperial Beach shoreline showed that shoreline station number 5, closest to the Tijuana River, is at higher risk for increased FIB densities during all ENSO events. In conclusion SST's was not a contributing factor to Imperial Beach shoreline contamination though rainfall was significant. There was no evidence that the SBOO caused contamination at the Imperial Beach shoreline during either ENSO event; conversely the Tijuana River was proven to be a reliable source.