A multidisciplinary approach was taken to assess the potential importance of groundwater seepage to nutrient inputs into Manila Bay, Philippines. Three lines of seepage meters were installed in transects along the coast at Mariveles, Bataan Province, during the period 8–10 January 2005. The overall average seepage flux was 5.1 ± 5.4 cm d⁻¹ (n = 73) with a range of 0–26 cm d⁻¹ and a calculated integrated shoreline flux of 12.4 m³ m⁻¹ d⁻¹. Additional methodologies employed included automatic seepage meters, resistivity measurements, sampling for nutrient analyses in both seepage meters and ambient seawater, and use of natural radon as a groundwater tracer. Seepage meter and tracer results provided consistent results of estimates of submarine groundwater discharge into Manila Bay. Many lines of evidence suggest that seepage fluxes are not steady state but are modulated by the tides. Resistivity profiles show that the saline-freshwater interface moves on a tidal timescale, consistent with the observed drop in salinity of the seepage waters as low tide approaches. Our results show that dissolved inorganic nitrogen (DIN) fluxes via submarine groundwater discharge are comparable in magnitude to DIN fluxes from each of the two major rivers that drain into Manila Bay.