This study investigated the processes responsible for perennial low pH in Nyaruzinga wetland water source in Western Uganda. Under anoxic conditions in wetlands, the redox potential and pH increase, thereby favouring dissolution of iron compounds, humic substances and release of copper, chromium, cobalt, nickel and lead. In situ temperature, pH, DO, EC and Eh were determined while the heavy metals, anions, cations, TOC, DOC and humic substances were analysed in the laboratory, for sediments, raw and treated water. The pH and DO increased from 70 cm deep in the wetland to the surface while the other parameters decreased. Copper (0.123-0.152 mg/L), chromium (0.002-0.299 mg/L), nickel (0.07-0.119 mg/L) and cobalt (0.006-0.081 mg/L) were determined at 70 cm deep, being trace (0.001-0.09 mg/L) at the wetland surface. High concentrations of TOC (14.7-28.3 mg/L) and DOC (0.03-0.71 mg/L) were measured in the wetland while traces of DOC (0.001-0.009 mg/L) and humic substances were determined in raw water but not in the treated water. The low pH in Nyaruzinga wetland is attributed to low molecular weight humic substances under perennial water logged conditions, and treatment processes should aim to remove them.