Dune slack habitats are highly dependent on the availability of water to support flora and fauna. Typically this is provided by shallow groundwater. This paper describes the seasonal and long term variation in groundwater levels in part of the Sefton coastline between 1972 and 2007. The effects of climate change, vegetation management and coastline realignment on groundwater levels are modelled. The observed annual water table levels rise and fall with an amplitude of 1.5 m, but longer term variations and trends are apparent. A stochastic water balance model was used to describe the changes in water table levels in slack floors in the open dunes and also in areas afforested with pine trees. It was found that the pine trees evaporated 214 mm/year more than open dunes vegetation, resulting in the water table being 0.5-1.0 m lower under the trees than under the open dunes. The effects of climate change on the ground water was simulated using predictions of future climate conditions based on the UKCIP02 medium high emissions scenario. The increase in temperature and change in rainfall patterns will result in a decrease in mean ground water levels by 1.0-1.5 mm in the next 90 years. Typical patterns consist of sequences of 5-10 years of low water table levels interspersed by infrequent sequences consisting of 2-5 years of relatively high or "normal" levels. These results indicate that that flora and fauna that cannot survive a 5-10 year period of water table levels >2.5 m below ground level are unlikely to survive or persist in many slack areas and a change in the ecology of these slack may become inevitable. Other effects of climate change include sea level rise which will result in a gradual rise in water table levels. Coastal erosion will increase the water table gradient to the sea and result in a slight lowering of the ground water levels. Conversely coastal accretion will reverse this process. The spatial distribution of coastal erosion and accretion along the Sefton coastline and its likely impacts on groundwater levels are discussed. The modelling work described in this paper has identified the factors which have the largest effect on groundwater levels in temperate coastal dune systems.