Coastal dunes support a biodiverse wetland habitat, dune slacks, which depend on a seasonally fluctuating, but near-surface, groundwater level. Any long-term change in the hydrological regime will impact the ecology. Analysis of long-term water level hydrographs, using a methodology prescribed for surface water flow gauging data, provides a set of ecohydrological ‘indicators of alteration’. These indicators collectively form a robust quantified measure of change that provides a basis for assessing the ecological impact that may result from a changed hydrological regime. This method was tested using monthly frequency water level data from three west coast UK coastal dunes, over periods of up to 37 years. Mean hydrological variables derived from the hydrographs were compared pre-impact and post-impact for a variety of perturbations: medium-term climate variation and pre-shoreline and post-shoreline erosion. The method provided a valid quantification of hydrological change. The low frequency of water-level data measurements compared with continuous flow-gauge data precluded analysis of change in inter-annual variability or perturbation (coefficients of variability) because of the likelihood of missed extreme flood and drought. Principal components analysis was used to identify associations between hydrological indicators and highlighted redundancy among some indicators such as measures of frequency and duration but orthogonality, i.e. independence, of others such as mean water levels and duration of drought. The hydrological effects of climatic variation over a 37-year period, of management interventions and erosion events that occurred at the three coastal dunes were small compared with the likely impact from projected climate change predictions. Copyright © 2012 John Wiley & Sons, Ltd.