Radon-222 is very concentrated in groundwater relative to surface waters and thus serves as an effective groundwater discharge tracer. We observed spikes in radon data from an earlier (2004) survey of the Chao Phraya River that appeared to correspond to locations where major canals (“klongs”) enter the river. We returned in 2006 and conducted more detailed surveys along some of the main klongs on the western (Thonburi) side of the Chao Phraya to evaluate this possibility. Our results show that both radon and conductivity are enriched in some areas of the klongs with 3 apparent “end-members,” two of which are likely related to groundwater seepage. Furthermore, nutrient analyses conducted during a time-series experiment at a site of suspected high discharge (Wat Intharam, Klong Bangkok Yai) showed that dissolved inorganic nitrogen (DIN) and phosphate correlated significantly to the groundwater tracer, radon. Rough estimates of the nutrient fluxes in this area are orders of magnitude higher than those measured in coastal settings and may represent a significant fraction of the riverine flux. It thus appears very likely that seepage of shallow groundwater is an important pathway for nutrient contamination of the klongs, and thus to the river, and ultimately to the Gulf of Thailand.