Time series analysis methods have been used to detect behavioral patterns in a set of nine time series. These series contained information in a 3‐h time step about meteorological, hydrological and tidal data of a sand dune pond area located in Doñana National Park in the southwest of Spain. The methods used, such as wavelet analysis and additive seasonal decomposition, had never been applied before in the types of ecosystems studied. These approaches have improved the current knowledge of the conceptual model of the Santa Olalla pond system, the only system with a permanent hydroperiod located in this protected area. In addition, complex surface water‐groundwater interactions, not visible through descriptive methods, have been distinguished to have a strong seasonal component. Finally, we evaluated the effect of pumping activity in a nearby coastal resort on the water supply of the Santa Olalla pond system. Although direct damage to this sand dune pond has not yet been identified, special attention must be paid in order to maintain groundwater inputs that are integral to maintaining its current status.