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The ice‐cover period in lakes is increasingly recognized for its distinct combination of physical and biological phenomena and ecological relevance. Knowledge gaps exist where research areas of hydrodynamics, biogeochemistry and biology intersect. For example, density‐driven circulation under ice coincides with an expansion of the anoxic zone, but abiotic and biotic controls on oxygen depletion have not been disentangled, and while heterotrophic microorganisms and migrating phytoplankton often thrive at the oxycline, the extent to which physical processes induce fluxes of heat and substrates that support under‐ice food webs is uncertain. Similarly, increased irradiance in spring can promote growth of motile phytoplankton or, if radiatively driven convection occurs, more nutritious diatoms, but links between functional trait selection, trophic transfer to zooplankton and fish, and the prevalence of microbial versus classical food webs in seasonally ice‐covered lakes remain unclear. Under‐ice processes cascade into and from the ice‐free season, and are relevant to annual cycling of energy and carbon through aquatic food webs. Understanding the coupling between state transitions and the reorganization of trophic hierarchies is essential for predicting complex ecosystem responses to climate change. In this interdisciplinary review we describe existing knowledge of physical processes in lakes in winter and the parallel developments in under‐ice biogeochemistry and ecology. We then illustrate interactions between these processes, identify extant knowledge gaps and present (novel) methods to address outstanding questions.

Winter is an important season for many limnological processes, which can range from biogeochemical transformations to ecological interactions. Interest in the structure and function of lake ecosystems under ice is on the rise. Although limnologists working at polar latitudes have a long history of winter work, the required knowledge to successfully sample under winter conditions is not widely available and relatively few limnologists receive formal training. In particular, the deployment and operation of equipment in below 0°C temperatures pose considerable logistical and methodological challenges, as do the safety risks of sampling during the ice‐covered period. Here, we consolidate information on winter lake sampling and describe effective methods to measure physical, chemical, and biological variables in and under ice. We describe variation in snow and ice conditions and discuss implications for sampling logistics and safety. We outline commonly encountered methodological challenges and make recommendations for best practices to maximize safety and efficiency when sampling through ice or deploying instruments in ice‐covered lakes. Application of such practices over a broad range of ice‐covered lakes will contribute to a better understanding of the factors that regulate lakes during winter and how winter conditions affect the subsequent ice‐free period.