A prospective cohort epidemiological pilot study was performed at three tropical beaches with point- and non-point-sources of fecal pollution to characterize the risk of illness among swimmers and non-swimmers. There was an increased risk of illness in swimmers as compared to non-swimmers, even when waters met current microbial standards for recreational water quality. Illnesses included gastrointestinal (GI), skin and respiratory symptoms, earache and fever. Odds ratios (ORs) ranged from 0.32 to 42.35 (GI illness), 0.69 to 3.12 (skin infections), 0.71 to 3.21 (respiratory symptoms), 0.52 to 15.32 (earache) and 0.80 to 1.68 (fever), depending on the beach sampled. The indicators that better predicted the risks of symptoms (respiratory) in tropical recreational waters were total (somatic and male-specific) coliphages (OR = 1.56, p < 0.10, R2 = 3.79%) and Escherichia coli (OR = 1.38, p < 0.10, R2 = 1.97%). The present study supports the potential of coliphages as good predictors of risks of respiratory illness in tropical recreational waters. This is the first study that has determined risks of illness after exposure to tropical recreational waters with point- and non-point sources of fecal contamination. The results give an opportunity to perform epidemiological studies in tropical recreational waters in Puerto Rico which can include more participants and other indicators and detection techniques.