Brunei Darussalam on the island of Borneo uses most of its water resources for drinking water purposes from surface water with less than 1% from groundwater. The Mengkubau reservoir is an important water resource for Brunei in this regard. Due to an increase in water demand the reservoir was upgraded and the dam height was increased by more than 3 meters in 2017. This study assesses the water quality of the Mengkubau reservoir over a five year time period between 2015 and 2020. This study shows that the increase in the dam height submerged previous oxic sediments causing the footprint of the reservoir to be increased by more than 30%. The analysis from water sampling confirms that the increase in iron and manganese in particular is a result of the reducing conditions which were established due to the increase in surface area of the reservoir. In particular manganese concentrations with values of up to 4 $mg/l$ are now exceeding guideline values. The analysis strongly indicated that both iron and manganese have a seasonal component. The change in water quality was accompanied by a change in pH values from a previous pH value of around 5 to a pH value of around 6.5. These changes were also confirmed with high frequency monitoring using a monitoring sonde. Here, nutrient levels such as nitrate, ammonium and blue green algae were assessed as well, which were all found to be comparably low and below guideline values. This study shows that the change in water quality in particular iron, manganese and pH due to the establishment of reducing conditions can have long-term effects on the water quality of a catchment. Future monitoring on the pathways and source of iron and manganese are recommended.