The EU Water Framework Directive dictates an integrated approach to surface water and groundwater resource assessment and management. The adequacy of existing groundwater models and surface process models for resource management purposes is reviewed, and is found wanting in areas where both surface water and groundwater flow processes are important. Thus there is a need for appropriate modelling tools to simulate near-surface processes and interface with groundwater models. The basic processes operating between precipitation and groundwater recharge are discussed, with particular consideration of rapid runoff, interflow and ‘runoff recharge’, which can result in delay and translocation of recharge. These processes are translated into an algorithmic scheme defined by only a small number of parameters, based on ideas current in the literature. The resulting scheme is sufficiently flexible to model both outcrop aquifers and those where rapid runoff, interflow and runoff recharge are also important. Calculations can be carried out for simple lumped catchments or on model grids so that the tool can be applied throughout model development as understanding improves, from initial lumped water balances to the generation of distributed stream flow and recharge input files for the MODFLOW groundwater flow code. An important consequence of this approach is that modelled river flows can be compared directly with gauged flows without the need for baseflow separation. The success of the algorithmic scheme is demonstrated by two examples: reproducing the results of an existing model of a limestone aquifer with perforated cover (where runoff recharge is particularly important); and by constructing a new model of a sandstone aquifer with complex top boundary conditions.