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The Wairau Plain in Marlborough, New Zealand, host a shallow, highly conductive gravel aquifer which is mainly recharged by the braided Wairau River. The groundwater of the Wairau Aquifer is an important source of drinking water in the region and provides irrigation water for viticulture. Managing the groundwater is increasingly challenging because of a decline in levels and spring flows combined with a natural seasonality and an expected high vulnerability to climate change and overexploitation.A prerequisite for groundwater managment and limit-setting is the knowledge of the water supply (recharge) as well as the water discharge and takes from the aquifer. Both are spatialy and temporally highly variable and difficult to measure. In addition, the aquifer is influenced by ephemeral streams which could potentially lead to unknown groundwater sinks and sources and periodical shifts of boundary locations.In order to investigate these aspects and to estimate the water balance components and fluxes in the associated groundwater system, a coupled surface water – groundwater flow model (MODFLOW) has been set up. A variety of observations, ranging from groundwater heads to spring/river flows and exchange rates, were built into the model. Metered groundwater abstraction data was used to test and adapt a spatio-temporally distributed soil water balance model that is coupled to the MODFLOW model.The complex surface flow network of the Wairau Plain and strong contrasts of hydraulic conductivity (up to 4 orders of magnitude) between older hydrogeological units and more recent, interwoven fluvial sediments have been a major challenge in the model setup. An iterative procedure with step-wise increasing complexity of parameterization was adopted to derive a plausible model structure, that is commensurable with the various observation types. Model parameters were calibrated and (linear) uncertainty bounds estimated using the PEST software.The model performs well with respect to the plausibility of the groundwater flow field and the overall water balance. Groundwater heads, river-groundwater exchange flows and spring flows are generally well covered by the predictive uncertainty bounds during the evaluation period (data not utilized for calibration). The model provides insights into the relative contributions and the seasonality of the various water balance components of the Wairau Aquifer. It has been confirmed that the Wairau River is the main contributor to groundwater recharge, but also that recharge in a given year is matched by equal levels of discharge to low-land springs and off-shore. Although large river flood events during the wet period lead to interim excess groundwater storage, the recession to pre-flood groundwater levels is surprisingly fast (less than one year). On the other hand, unremarkable (high return period) flood events in the summer period, which keep river flows at elevated levels, have a noticeable effect on groundwater storage. This effect can last up until the following dry season.The model proved useful for assessing the status quo of the Wairau Aquifer groundwater resources. This is a prerequisite for the search and testing of alternative management options that are imminent due to the observed trends in groundwater levels.