Climate change is leading to shifts in not only the average timing of phenological events, but also their variance and predictability. Increasing phenological variability creates a stochastic environment that is critically understudied, particularly in aquatic ecosystems. We provide a perspective on the possible implications for increasingly unpredictable aquatic habitats, including more frequent trophic asynchronies and altered hydrologic regimes, focusing on ice-off phenology in lakes. Increasingly frequent phenological extremes may limit the ability of organisms to optimize traits required to adapt to a warming environment. Using a unique, long-term ecological dataset on Escanaba Lake, WI, USA, as a case study, we show that the average date of ice-off is shifting earlier and becoming more variable, thus altering limnological conditions and yielding uncoupled food web responses with ramifications for fish spawn timing and recruitment success. A genes-to-ecosystems understanding of the responses of aquatic communities to increasingly variable phenology is needed. Our perspective suggests that management for diversity, at the intra- and interspecific levels, will become paramount for conserving resilient aquatic ecosystems.