With increasing demand being placed on water resources the efficient use of water is inevitable to increase rice productivity. The availability of water through a catchment can vary significantly with some water being used in upstream irrigation activities, for environmental flows, groundwater and infiltration movements, all resulting in challenges and costs for irrigators accessing water for their production systems. The use of tubewells, dams and groundwater extraction to access available water requires substantial capital investments. In addition, the production, transportation and application of pumps and pipes, and the associated fuels and oils needed to run them emit significant quantities of greenhouse gases (GHG). In this study, we analysed the GHG and water productivity implications of water reuse through pumping groundwater and creek water and compare this with canal irrigation systems under gravity-fed irrigation in the Upper Pumpanga River Integrated Irrigation System, in the Philippines. The results show that around 30% of total surface water applied was reused by internal check dams and pumping from shallow groundwater. The analysis indicates water reuse contributes significantly to water productivity; however, it does increase GHGs through pumping. The total amount of GHG emissions from pump irrigation system (with water reuse) is around 1.47 times higher than that of canal irrigation systems (without water reuse). Based on the finds, high priority on water reuse should be given only to the areas where water scarcity is a serious issue.