This dataset contains physical, chemical and ecological data collected between 2018-2019 at the deepest point of Elterwater’s inner basin. Profiles of chlorophyll, dissolved oxygen, and light and Secchi disk extinction depth were collected at weekly scale during the stratified period and fortnightly/monthly timescale outside of this period. Water temperature profiles were collected at 15-minute intervals, and hourly averaged. The work was supported by the Natural Environment Research Council (Grant NE/ L002604/1).