Abstract  Water quality monitoring in Hanalei Bay, Kaua`i (Hawai`i, USA) has documented intermittent high concentrations of nutrients (nitrate, phosphate, silica, and ammonium) and fecal indicator bacteria (FIB, i.e., enterococci and Escherichia coli) in nearshore waters and spurred concern that contaminated groundwater might be discharging into the bay. The present study sought to identify and track sources of nutrients and FIB to four beaches in Hanalei Bay and one beach outside the bay, together representing a wide range of land uses. ²²³Ra and ²²⁴Ra activity, salinity, nutrient and FIB concentrations were measured in samples from the coastal aquifer, the nearshore ocean, springs, the Hanalei River, and smaller streams. In addition, FIB concentrations in beach sands were measured at each site, and the enterococcal surface protein (esp) gene assay was used to investigate whether the observed FIB originated from a human source. Nutrient concentrations in groundwater were significantly higher than in nearshore water, inversely correlated to salinity, and highly site specific, indicating local controls on groundwater quality. Fluxes of groundwater into Hanalei Bay were calculated using a mass-balance approach and represented at least 2–10% of river discharges. However, submarine groundwater discharge (SGD) may provide 2.7 times as much nitrate + nitrite to Hanalei Bay as does the Hanalei River. It may also provide significant fluxes of phosphate and ammonium, comprising 15% and 20% of Hanalei River inputs, respectively. SGD-derived silica inputs to the bay comprised less than 3% of Hanalei River inputs. FIB concentrations in groundwater were typically lower than those in nearshore water, suggesting that significant FIB inputs from SGD are unlikely. Positive esp gene assays suggested that some enterococci in environmental samples were of human fecal origin. Identifying how nutrients and FIB enter nearshore waters will help environmental managers address pressing water quality issues, including exceedances of the state Enterococcus water quality standard and nutrient loading to coral reefs.