Lakes are disproportionately important ecosystems for humanity, containing 77% of the liquid surface freshwater on Earth and comprising key contributors to global biodiversity. With an ever-growing human demand for water and increasing climate uncertainty, there is pressing need for improved understanding of the underlying patterns of natural variability of water resources and consideration of their implications for water resource management and conservation. Here we use Bayesian harmonic regression models to characterise water level dynamics and study the influence of cyclic components in confounding estimation of long-term directional trends in water levels in natural Irish lakes. We found that the lakes were characterised by a common and well-defined annual seasonality and several inter-annual and inter-decadal cycles with strong transient behaviour over time. Importantly, failing to account for the longer-term cyclic components produced a significant overall underestimation of the trend effect. Our findings demonstrate the importance of contextualising lake water resource management to the specific physical setting of lakes.