Water temperature plays a primary role in controlling a wide range of physical, geochemical and ecological processes in lakes, with considerable influences on lake water quality and ecosystem functioning. In this paper, we report on the ability of the one-dimensional lake model to simulate the water temperature of Moroccan lakes, i.e., Sidi Boughaba and Sidi Ali lakes, over a 35 yrs period from 1979 to 2014, affected by climate change and based on a freshwater lake model (FLake). During the study periods, two variables are studied, the epilimnion and metalimnion temperatures. The result analysis shows that epilimnion temperatures increased, while metalimnion temperatures decreased. Additionally, we calculate significant air temperature, wind speed and water temperature variation and illustrate, using a sequential t test analysis of regime shifts (STARS) based on the Rodionov method, a substantial increase in annually averaged of all variables, in response to an abrupt shift in the climate. Schmidt stability showed a significant increase for Sidi Ali Lake and near 0 for Sidi Boughaba Lake. On the other hand, the sensitivity analysis (i.e., one-at-a-time (OAT) method) of the atmospheric variable is discussed. The results show good agreement with water temperature observations that suggests that the predictive model can be used to obtain a firstorder estimation of water temperature in Moroccan lakes. Hence, it is possible to apply this model in other Moroccan lakes to simulate the behavior of temperature and to investigate the potential future warming of the water column in lakes, affected by climate change.