A cold thermoregulatory model (CTM) was applied to data from partially immersed subjects divided into normal (NF) or low fat (LF) groups in order to validate CTM during immersion at two depths and to examine mechanisms underlying the individual differences. CTM defines thermal characteristics, e.g. surface area and maximal shivering intensity, using height, weight, fat %, age and VO2max. Ten clothed subjects, 5 NF (15–19%) and 5 LF (8.1–14.7%), were immersed in both 10 and 15°C water at chest (CH) and waist (WA) level. Environmental and clothing inputs for CTM were weighted to adjust for the ratio of skin surface area covered by either air or water at various immersion depths. Predicted core temperature (T c) responses for each individual trial were compared with measured data. There were no significant differences (P > 0.05) between measured T c and predicted T c for NF at all four conditions. In contrast, for the LF group, the predicted T c responses were all higher than measured (P < 0.05). However, predicted T c agreed closer with measured T c for LF when leg muscle blood flow was increased in the simulation. This suggests that blood flow may contribute to the rapid decline in T c observed in LF and its variance may cause in part the individual differences in T c responses. CTM predicts T c responses to immersion at various depths with acceptable accuracy for NF individuals in this study and can be adapted to non-uniform environments.