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We investigated processes contributing to periodic acidification events in headwater streams of Nee Soon Forest Catchment (NSFC) in Singapore by monitoring hydrochemical changes in response to rainfall inputs. Stream chemistry response to most rainfall events was characterized by decreases in pH from means ranging from 5.1 to 5.3 to below 4.8–5.0 and corresponding increases in specific electrical conductivity from baseflow values of 15–30 to 50–80 μS cm−1, indicative of low-total dissolved solids in stormflow. The decreases in pH in the streams, which are typically acidic year-round, were related to occasional highly acidic rainfall inputs (pH ~4.05) and likely the flushing of organic acids into the stream by shallow subsurface flow interacting with surface litter and/or organic-rich soil horizons. The interaction of rainwater runoff with organic matter in the soil matrix possibly alters the chemical composition of stormflow, influencing pH. Decomposition of instream organic matter also reduces stream water pH. Leaching experiments revealed that the overland flow passing through organic matter and A horizon material has the potential to lower stream water pH by approximately a half unit or more, in part, by flushing nitrates that were produced by microbial decomposition of organic matter and/or precipitated sulphur that enterred the forest by wet or dry atmospheric deposition. The observed periodic acid events are a natural phenomenon in the stream system in this urban environment because of naturally acidic rainfall and granitic soils with low buffering potential. However, acid events are likely amplified in frequency and magnitude by anthropogenic pollution emissions of sulphur and nitrogen species (e.g., SO2 and NOx) from local and regional sources that lower rainfall pH. Although, acid runoff events are typically short-lived (