Abstract: In order to reveal the diatom diversity patterns and aquatic ecological environment of the different types of lakes in the Ningwu alpine lake group in northern Shanxi Province, lake diatom assemblage composition, diatom diversity indices and their relationship with their concomitant environmental factors in deep Lake Gonghai and shallow Lake Pipahai were analyzed. The results show that: (1) The lower diatom diversity index in Lake Pipahai corresponds primarily to its higher total nitrogen (TN) level, so TN is probably the dominant factor influencing the biodiversity of the two lakes. (2) Compared with the ice-covered period in 2016, the diatom diversity indices of Lake Gonghai in the frozen period of 2017 were significantly lower, corresponding to the higher total phosphorus (TP) and TN concentrations. The diatom diversity index can be used as an index for lake environmental quality assessment. (3) There are common diatom species, namely Lindavia radiosa and Pantocsekiella ocellata, in the two lakes. However, Lindavia radiosa flourished in Lake Gonghai when TP concentration was higher in the frozen period of 2017, whereas its relative abundance was higher when TN concentration was higher in the frozen period of 2016 in Lake Pipahai. The species may be used as an indicator species for lake environmental quality assessment. (4) During the summer thermal stratification period in Lake Gonghai, the diatom diversity index was lower than that during the spring and autumn mixing periods; whereas, Lake Pipahai was well mixed throughout the open-water period due to the shallow water depth, and the diatom diversity index has subtle fluctuations. This study reveals that the diatom seasonal patterns and ecological environmental changes differ in the different types of lakes in the Ningwu alpine lake group. To mitigate algal bloom in the circumstance of future climate warming and increased human disturbance, diatom seasonal patterns and ecological environmental changes differ in the different types of lakes in the Ningwu alpine lake group, and more attention need to be paid to the biological and environmental monitoring of shallow Lake Pipahai particularly in summer.