Timely information on the availability of water and forage is important for the sustainable development of pastoral regions. The lack of such information increases the dependence of pastoral communities on perennial sources, which often leads to competition and conflicts. The provision of timely information is a challenging task, especially due to the scarcity or non-existence of conventional station-based hydrometeorological networks in the remote pastoral regions. A multi-source water balance modelling approach driven by satellite data was used to operationally monitor daily water level fluctuations across the pastoral regions of northern Kenya and southern Ethiopia. Advanced Spaceborne Thermal Emission and Reflection Radiometer data were used for mapping and estimating the surface area of the waterholes. Satellite-based rainfall, modelled run-off and evapotranspiration data were used to model daily water level fluctuations. Mapping of waterholes was achieved with 97% accuracy. Validation of modelled water levels with field-installed gauge data demonstrated the ability of the model to capture the seasonal patterns and variations. Validation results indicate that the model explained 60% of the observed variability in water levels, with an average root-mean-squared error of 22%. Up-to-date information on rainfall, evaporation, scaled water depth and condition of the waterholes is made available daily in near-real time via the Internet (http://watermon.tamu.edu). Such information can be used by non-governmental organizations, governmental organizations and other stakeholders for early warning and decision making. This study demonstrated an integrated approach for establishing an operational waterhole monitoring system using multi-source satellite data and hydrologic modelling.