The Doñana National Park (DNP) is a protected area with water resources drastically diminishing due to the unsustainable extraction of groundwater for agricultural irrigation and human consumption of a nearby coastal city. In this study, we explore the potential of wavelet analysis applied to high-temporal-resolution groundwater-and-surface-water time series of temporary coastal ponds in the DNP. Wavelet analysis was used to measure the frequency of changes in water levels and water temperature, both crucial to our understanding of complex hydrodynamic patterns. Results show that the temporary ponds are groundwater-dependent ecosystems of a through-flow type and are still connected to the sand-dune aquifer, regardless of their hydrological affection, due to groundwater withdrawal. These ponds, even those most affected by pumping in nearby drills, are not perched over the saturated zone. This was proven by the evidence of a semi-diurnal (i.e., 6 h) signal in the surface-level time series of the shallow temporary ponds. This signal is, at the same time, related to the influence of the tides affecting the coastal sand-dune aquifer. Finally, we detected other hydrological processes that affect the ponds, such as evaporation and evapotranspiration, with a clear diurnal (12 h) signal. The maintenance of the ecological values and services to the society of this emblematic wetland is currently in jeopardy, due to the effect of the groundwater abstraction for irrigation. The results of this study contribute to the understanding of the behavior of these fragile ecosystems of DNP, and will also contribute to sound-integrated water-resource management.