Quantifying groundwater availability depends upon sound methods and the use of integrated models. To determine availability or sustainable yield, the influence of scientific uncertainty from key sources, such as anthropogenic recharge, must be considered. This study evaluates uncertainty in recharge interpretations on the modeled available water balance for an urban case in Texas, USA. Analyses are completed using the Groundwater Decision Support System, which is a research code-base for an integrated modeling. The case study develops spatially and temporally resolved recharge interpretations based on NEXRAD precipitation and detailed land use data. Results demonstrate the implications of scientific uncertainty as it influences recommendations for policy and urban water management decisions that are based on modeled outputs. Geospatial methods account for spatial and temporal components and can be replicated for other systems. These methods are also useful for resolving uncertainty in relation to the influence of urbanization on recharge through land use change.