This dataset consists of physical, chemical and ecological water quality variables collected at Blelham Tarn during 2016-2017. Profiles for the following variables were collected on a weekly scale during the stratified period of the lake and fortnightly or monthly timescales outside of the stratified period; light, chlorophyll a (phytoplankton biomass proxy), temperature, specific conductivity, phycocyanin (cyanobacteria pigment), pH and oxygen (mg/l and percentage saturation). The secchi depth was also collected at the same sampling frequency. Phytoplankton taxonomy and biovolumes were collected at 1-6 m June-November 2016 at a weekly interval. Nutrient profiles (nitrogen, phosphorus and silica) were collected on a monthly timescale in June-October 2016. In addition to lake data, samples from three lake inflows and the outflow were collected for nutrients (nitrogen, phosphorus and silica) at monthly intervals along with discharge. Water level and water temperature were also recorded at a 15 minute frequency at one inflow and the outflow.