AbstractGroundwater recharge is the main forcing of regional groundwater flow. In traditional partial‐differential‐equation (pde)‐based models that treat aquifers as separate compartments, groundwater recharge needs to be defined as a boundary condition or it is a coupling condition to other compartments. Integrated models that treat the vadose and phreatic zones as a continuum allow for a more sophisticated calculation of subsurface fluxes, as feedbacks between both zones are captured. However, they do not contain an explicit groundwater‐recharge term so it needs to be estimated by post‐processing. Groundwater recharge consists of changes in groundwater storage and of the flux crossing the water table, which can be calculated based on hydraulic gradients. We introduce a method to evaluate the change of groundwater storage by a time‐cumulative water balance over the depth section of water table fluctuations, avoiding the use of a specific yield. We demonstrate the approach first by a simple 1‐D vertical model that does not allow for lateral outflow and illustrates the ambiguity of computing groundwater recharge by different methods. We then apply the approach to a 3‐D model with a complex topography and subsurface structure. The latter example shows that groundwater recharge is highly variable in space and time with notable differences between regional and local estimates. Local heterogeneity of topography or subsurface properties results in complex redistribution patterns of groundwater. In fully integrated models, river‐groundwater exchange flow may severely bias the estimate of groundwater recharge. We, therefore, advise masking out groundwater recharge at river locations.