Changes in land cover can have negative impacts on the hydrological and hydraulic processes in river basins and watersheds such as increase in surface runoff and peak flows, and greater incidence, risk and vulnerability of flooding. In this study, the impacts of land-cover changes to the hydrologic and hydraulic behaviours of the Agusan River Basin (ARB), the third largest river basin in the Philippines, was analysed using an integrated approach involving Remote Sensing (RS), Geographic Information System (GIS), and hydrologic and hydraulic models. Different land-cover classes in the ARB for the years 1995 and 2017 were mapped using Landsat 5 TM and Landsat 8 OLI images. Using a post-classification change detection approach, changes in land-cover were then determined. The impacts of these changes in land-cover to the to the basin discharge were then estimated using a calibrated hydrologic model based on the Hydrologic Engineering Center - Hydrologic Modeling System (HEC-HMS) under different extreme rainfall conditions. The impact of the changes in land-cover to flood depth and extent was also determined using a hydraulic model based on the HEC-RAS (River Analysis System). Land cover classification results revealed that the ARB is 67.7% forest in 1995 but have decreased to 62.8% in 2017. Agricultural areas in the basin were also found to have increased from 12.2% to 15.5% in the same period. Other notable land cover changes detected include the increase in built-up lands and range lands, and decrease in barren lands. HEC HMS and HEC RAS model simulation results showed that there was an increase in discharge, flood depth, and flood extents between 1995 and 2017, implying that that the detected changes in land cover have negative impacts to hydrologic and hydraulic behaviours of the ARB.