The dynamics of spatial heterogeneity of Lake Surface Water Temperature (LSWT) at sub-pixel satellite scale O(1 m) and its effect on the surface cooling estimation at typical satellite pixel areas O(1 km2) were investigated using an airborne platform. The measurement platform including (i) a thermal imagery package suspended from a balloon (called BLIMP), and (ii) an autonomously operating catamaran (called ZiviCat) for in situ measurements, was used to obtain LSWT maps resolved at sub-pixel scales. The data include: (i) The thermal registered maps for four selected missions, called MGL1 (18 March 2016), EGL2 (19 July 2016), MGL2 (20 October 2016) and MGL3 (29 March 2017), measured by BLIMP and ground-truthed by ZiviCat measurements. (ii) The LSWT and air temperature measurements of EGL2, MGL2 and MGL3 missions for a 30-min duration covering the BLIMP imagery time used for sensitivity analysis of the results. The surface cooling model used in this study is based on a validated and calibrated model at two locations on Lake Geneva (https://doi.org/10.1002/lom3.10267).