The aim of this research was the analysis of the effect of a dam height raise on the water quality of a tropical reservoir used for drinking water purposes in South East Asia. Analyses of iron, manganese, pH and ammonia were performed over a 5-year period from daily water sampling at the reservoir. In addition, high-frequency monitoring data of nitrate, ammonium, pH and blue-green algae were obtained using a monitoring probe. The results showed that due to the raising of the reservoir water level, previously oxic sediments became submerged, triggering an increase in iron and manganese in particular due to the establishment of reducing conditions. Manganese concentrations with values up to 4 mg L−1 are now exceeding guideline values. The analysis strongly indicated that both iron and manganese have a seasonal component with higher iron and manganese concentrations during the wet season. Over a three-year period afterwards, concentrations did not go back to pre-raise levels. The change in water quality was accompanied by a change in pH from previous values of around 5 to pH values of around 6.5. Geochemical simulations confirmed the theory that the increasing concentrations of iron and manganese are due to the dissolution of MnO2 and ferric oxyhydroxides oxidising organic matter in the process. This study showed that changes in reservoir water levels with the establishment of reducing conditions can have long-term effects on the water quality of a reservoir.