Uncertainty about the H+ buffering capacity in tropical rain forest limits our ability to predict the future effect of anthropogenic deposition on the streamwater chemistry. Export of major ions to the stream and the ion-fluxes via rainfall, throughfall, litter-leachate and soil-water pathways were observed to examine the source of streamwater nutrients in a small catchment in Sabah, Malaysia. The streamwater and the ion-fluxes were measured for 3.75 and 2 y, respectively, by collecting water twice a month and setting ion-exchange-resin columns. Streamwater pH ranged from 6.5 to 7.6 and was not sensitive to water discharge controlling base cations. The NO3−-N, Ca2+ and Mg2+ fluxes were low in atmospheric depositions (0.6, 0.5 and 0.3 kg ha−1 y−1, respectively) and markedly increased in the litter layer. The NO3−-N flux decreased drastically from subsoil (70 kg ha−1 y−1) to the stream (1.4 kg ha−1 y−1) whereas the Ca2+ and Mg2+ fluxes were not different between subsoil (38 and 18 kg ha−1 y−1) and stream (30 and 15 kg ha−1 y−1). Neutral pH in tropical streams was mainly due to the base cation leaching with deep chemical weathering in deeper strata, and a rapid decrease in NO3− leaching from the subsoil to the stream.