The increasing competition for water resources requires a better understanding of flows, fluxes, stocks, and the services and benefits related to water consumption. This paper explains how public domain Earth Observation data based on Moderate Resolution Imaging Spectroradiometer (MODIS), Second Generation Meteosat (MSG), Tropical Rainfall Measurement Mission (TRMM) and various altimeter measurements can be used to estimate net water production (rainfall (P) > evapotranspiration (ET)) and net water consumption (ET > P) of Nile Basin agro-ecosystems. Rainfall data from TRMM and the Famine Early Warning System Network (FEWS-NET) RainFall Estimates (RFE) products were used in conjunction with actual evapotranspiration from the Operational Simplified Surface Energy Balance (SSEBop) and ETLook models. Water flows laterally between net water production and net water consumption areas as a result of runoff and withdrawals. This lateral flow between the 15 sub-basins of the Nile was estimated, and partitioned into stream flow and non-stream flow using the discharge data. A series of essential water metrics necessary for successful integrated water management are explained and computed. Net water withdrawal estimates (natural and humanly instigated) were assumed to be the difference between net rainfall (Pnet) and actual evapotranspiration (ET) and some first estimates of withdrawals—without flow meters—are provided. Groundwater-dependent ecosystems withdraw large volumes of groundwater, which exceed water withdrawals for the irrigation sector. There is a strong need for the development of more open-access Earth Observation databases, especially for information related to actual ET. The fluxes, flows and storage changes presented form the basis for a global framework to describe monthly and annual water accounts in ungauged river basins.