A characteristic feature of ground penetrating radar (GPR) surveys on polythermal glaciers is an internal reflection presumably caused by the cold temperate transition surface (CTS), hence providing a possible tool for mapping thermal structure with high accuracy. Comparison of detailed temperature measurements in bore holes and GPR profiles at 345 MHz and 800 MHz center frequencies on Storglaciären, Sweden, show that the CTS can be detected and mapped with an accuracy of about ±1 m at both frequencies. A comparison between comprehensive GPR surveys of the cold surface layer, separated by 12 years (1989–2001), shows a substantial and complex thinning of the cold layer. An overall decrease of 8.3 m (22% of average thickness) of the CTS depth is much larger than uncertainties in CTS depth determinations. The stability of the cold surface layer depends on the net ice ablation at the surface and the downward migration of CTS. There is no evidence of substantial increased net ablation between the survey dates that could explain the observed thinning. However, small increase in average winter air temperature, a limiting factor for the temperature gradient through the cold surface layer, may provide a partial explanation. The weaker temperature gradient reduces the transport of latent heat from the CTS, thus slowing down its downward migration.