In the context of climatic uncertainty and potential climatic change, incorporating climatic variability and change in eco-hydrological analysis, as well as understanding the impact of such variability on ecosystems, is of crucial importance. The latter is particularly true for those complex ecosystems, such as wetlands, which cradle large varieties of species, many of which rare or endangered. Focusing on the Everglades wetlands, we investigate the presence of non-stationary elements in the seasonal cycle of precipitation, temperature and stage level and examine their correlation and potential impact on the ecosystem's flora and fauna. To this aim, we revisit demodulation techniques and demonstrate their validity for the diagnosis of long-term trends in the amplitude and phase of seasonal patterns of hydrologic series. We then analyse historical records of fauna and flora components of the Everglades in order to reveal potential relationships with hydrological trends. We observe that the seasonal patterns of all the time series analysed are non-stationary. In addition, we observe that the amplitude of seasonal oscillations of all hydro-climatic drivers is strongly correlated with anomalies in records of wading birds population and plant carbon assimilation. Copyright (c) 2014 John Wiley & Sons, Ltd.