The Baro Akobo River, Gambella, is a representative of lower Baro River watersheds with lost soils. Under eight landscapes, the geospatial and temporal variability of water use efficiency (WUE) and system WUE (sWUE) was investigated. In contrast with WUE, sWUE takes runoff into account, better capturing the combined effects of soil management, climate change, and land cover change on agricultural irrigation systems. The total area of the lower Baro River is 20,325. This study used GIS, RS, EasyFit, and CROPWAT8.0 software. It allows automatic fitting distributions to the data, selects the best mathematical tool, and quantifies the yields and WUE/sWUE. sWUE is a more helpful index than WUE to describe differences in water holding capacity and yield across agricultural landscapes. sWUE varies in streamflow from its correlation with runoff, with a coefficient of variation (CV) of 71% across the watershed. Evapotranspiration (ET) had a CV of 70%. Temporally, sWUE will decrease by 10% by 2050, but its spatial variability will reach 25%. These methods improve soil infiltration and water storage, which reduce runoff and standing water lost through ET and raise sWUE.