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The Wairau River is situated in the Marlborough Region in the North of New Zealand's South Island. Near its mouth into the Pacific Ocean, the river is recharging a regionally important aquifer which is managed for drinking water production in the Blenheim region and for irrigation of New Zealand's largest wine growing area. The Wairau Plain Aquifer is almost exclusively recharged by the Wairau River and closely related to its hydrological regime. The groundwater levels and spring flows at the Wairau Plain Aquifer have shown progressive decline in the past decades. This study analyses potential factors to explain this trend and a change in the hydrological regime using a combination of field investigations and a detailed numerical flow model. Results indicate that the driving forces of the system, rainfall and runoff, exhibit not only a strong interannual variability but seem to be also correlated with longer climate oscillations. The groundwater storage is also affected by strong seasonal variations and is particularly vulnerable to the frequency and duration of low-flow periods in summer. Climate variability alone, however, does not explain the log-term trends in storage. Another factor is the erosion of the Wairau River bed which can lead to a permanent loss of storage capacity and is caused by the effects of river training but also by extreme flood events. Another factor that should be taken into consideration is groundwater abstraction for irrigation, which accounts only for 1% of the total estimated storage, but up to 20% of the "live" manageable storage.The better understanding of the mechanisms and factors controlling the Wairau Plain Aquifer contributes to the identification of adaptation strategies for a sustainable management of the groundwater resources.