In-lake temperature data for a peatland headwater lake of the Conwy catchment, North Wales are presented from November 2006 until December 2008. The Lake for which the data represents is Llyn Conwy situated on the Migneint blanket bog within Snowdonia National Park. The data is from a temperature string suspended from a buoy anchored above the deepest part of the lake. Temperature is recorded at 2 metre intervals throughout the lake profile from 1 to 19 m. The purpose of this data is to investigate water column stability and to determine when, and to what degree stratification/mixing occurs and to make inferences about the effect of this on productivity, nutrient and chemical cycling. Note: there are gaps in this data set due to equipment/battery failures and/or freezing of the lake surface which meant it was not accessible.