Extreme weather threatens livelihood and urban development in the Philippines. However, addressing their effects and occurrences is a significant challenge, particularly in the Cagayan River Basin (CRB), due to increasing population and the dilemma of dam operations for floods and droughts management. Therefore, this paper focuses on investigating the impact of climate change on extreme weather events and understanding flood characteristics by simulating Typhoon Ulysses on the Magat dam. The Mann-Kendall test was used to investigate the spatiotemporal variability and magnitude of change in extremes over historical and future periods. Furthermore, Rainfall-Runoff Inundation Model was evaluated with four different dam operation scenarios to investigate mitigation strategies for dam optimisation to reduce flood and drought risks. Findings indicate an increased risk of dry and wet spells in future, potentially increasing vulnerability to drought and flooding over CRB. We also discovered that each sub-basin had different hydrological responses and significantly higher runoff than others. However, with a modified Magat dam operation to start a flow rate of 700 m3/s and a discharge rate of 0.5, the water level at Buntun can be lowered by 0.5 m. In addition, a proposed dam at Cagayan Segment 1 is expected to reduce flood risk in downstream areas.