Climate change poses significant risks to flood-prone regions, such as the Marikina River Basin in the Philippines, by altering key hydrological variables like rainfall and temperature. Understanding these impacts is crucial for developing effective flood risk management and drought mitigation strategies. This study assesses the potential effects of climate change on streamflow by comparing historical observations with future climate projections using the SWAT+ model. Daily weather data (1995–2012) from the Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA) and the National Aeronautics and Space Administration – Prediction of Worldwide Energy Resource (NASA-POWER) were used for streamflow model calibration and validation. Calibration with observed monthly discharge data from the Sto. Niño Station (2005–2008) yielded an NSE of 0.742 and a PBIAS of −0.198%, while validation with data from 2010–2012 resulted in an NSE of 0.555 and a PBIAS of 18.296%. The calibrated model parameters were then applied to future climate projections. Climate scenarios RCP4.5 and RCP8.5 were assessed under normal, dry, and wet year conditions by modifying rainfall and temperature inputs. Results indicate significant variability, with wet years showing increased discharge and dry years showing reduced discharge. Under normal conditions, RCP4.5 projected lower discharge, whereas RCP8.5 indicated higher discharge and more extreme fluctuations. The findings provide valuable insights for flood risk management and drought mitigation in the Marikina River Basin, supporting future climate adaptation efforts in tropical urbanizing basins.