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Climate-change is rapidly and intensively altering aquatic communities and habitats. While previous work has focused on direct effects of potential drivers, indirect and interactive effects on organisms and ecosystems have received less attention. Here, we give an overview of contributions to a special issue in Limnology and Oceanography that addresses this knowledge gap. Contributions covered diverse habitats, from polar to tropical regions, alpine streams to coral reefs. Several studies relied on time-series to identify indirect effects, thus emphasizing our need to maintain high-quality time-series data. Time-series are particularly crucial now that the pace of climate-change on aquatic-ecosystems is accelerating. Another common theme is the role of species-specific characteristics in physiology, behavior or genetics in aquatic ecosystem function. The addition of inter- and intra-specific variability to investigations of climate-change may be challenging particularly since ecosystem studies typically involve a large parameter space of environmental and biological variables across spatial and temporal scales. However, the results demonstrate that inclusion of species-specific dynamics, although challenging, can deliver mechanistic insights into aquatic ecosystem patterns and processes. Some contributions leverage habitat changes from disturbances or climate shifts to document capacity for resilience or recovery of pelagic and benthic communities. Jointly, the results in this special issue document fruitful approaches and provide urgent information needed for deciphering aquatic ecosystem responses to climate forcings. This information is foundational if we wish to tackle the combined effects of climate change and other human impacts with maximum efficacy and minimize unintended consequences for biodiversity and ecosystem functioning.