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1 Study Region: The unconfined Wairau Aquifer in the Marlborough District of New Zealand is almost exclusively recharged by the Wairau River and serves as the major resource for drinking water and irrigation in the region. A declining trend in aquifer levels and low-land spring flows has been observed for the past decades. 2 Study Focus: The aim of this study is to identify and analyse natural and anthropogenic factors controlling the hydrological regime of the Wairau Aquifer. Concurrent trends in the long-term water balance components for the Wairau catchment and in low-flow statistics as well as the correlation between hydro-meteorological drivers and the Interdecadal Pacific Oscillation (IPO) index were investigated. The impact of river morphology changes on river recharge rates was studied using a previously developed groundwater flow model. 3 New Hydrological Insights for the Region: Our study found that long-term trends in declining catchment-scale precipitation are superimposed on climate oscillation and a strong annual variability. Jointly, these processes have resulted in lower than average river flows, increased low-flow periods, and consequently in lower rates of aquifer recharge. River engineering caused erosion of the braided river morphology, leading to a possibly permanent loss of aquifer storage. Groundwater abstraction is not accurately known which is a limitation of this study. This additional information and adaptation strategies are required for sustainable management of the groundwater resources.