The chemical composition of ground waters and stream waters is thought to be determined primarily by weathering of parent rock. In relatively young soils such as those occurring in most temperate ecosystems, dissolution of primary minerals by carbonic acid is the predominant weathering pathway that liberates Ca2+, Mg2+ and K+ and generates alkalinity in the hydrosphere. But control of water chemistry in old and highly weathered soils that have lost reservoirs of primary minerals (a common feature of many tropical soils) is less well understood. Here we present soil and water chemistry data from a 10,000-hectare watershed on highly weathered soil in the Brazilian Amazon. Streamwater cation concentrations and alkalinity are positively correlated to each other and to streamwater discharge, suggesting that cations and bicarbonate are mainly flushed from surface soil layers by rainfall rather than being the products of deep soil weathering carried by groundwater flow. These patterns contrast with the seasonal patterns widely recognized in temperate ecosystems with less strongly weathered soils. In this particular watershed, partial forest clearing and burning 30 years previously enriched the soils in cations and so may have increased the observed wet season leaching of cations. Nevertheless, annual inputs and outputs of cations from the watershed are low and nearly balanced, and thus soil cations from forest burning will remain available for forest regrowth over the next few decades. Our observations suggest that increased root and microbial respiration during the wet season generates CO2 that drives cation-bicarbonate leaching, resulting in a biologically mediated process of surface soil exchange controlling the streamwater inputs of cations and alkalinity from these highly weathered soils.