This dataset contains under-ice physicochemical data from Missisquoi Bay and Shelburne Pond in Vermont, USA collected during the 2013-2014 and 2014-2015 winters and spring thaw periods. The main dataset contains data for ice depths, water column sampling depths, nutrient chemistry, chlorophyll a, and relevant physicochemical variables. Ancillary data includes nearby air temperature data for the study periods as well as river discharge data for contributing or nearby tributaries. Data collection is complete.