The population dynamics of diatoms are affected by a variety of environmental variables. Due to their short generation times and high sensitivity to changes in physicochemical conditions, diatoms are considered good environmental indicators. The main goal of our study was to find and explain the relationships between changes in meteorological conditions and diatom fluxes and taxonomic composition based on the example of two small lakes: Łazduny and Rzęśniki. Using meteorological data, sediment traps, and regular measurements of limnological and hydrochemical properties of the water column, we collected a three-year-long, high-resolution series of observations. The results show that total diatom fluxes are indirectly influenced by changes in meteorological conditions, acting through changes in the mixing regimes that determine the nutrient and light availability in lakes. Statistical analyses showed that the variability of the diatom data is correlated with air temperature and wind speed. Nevertheless, their influence on diatom assemblages is most likely the surrogate for the complex changes in the physical structure of the investigated lakes. Despite many similarities between the studied lakes such as mixing regime patterns, dominant diatom taxa, and seasonal dynamics of diatom fluxes, we recorded differences in both the seasonal succession of specific diatom taxa and the occurrence of the peaks of total fluxes, and differences in taxonomic composition referring to less dominant taxa. We attribute these dissimilarities to the local conditions, such as the hydrological types of the lakes, the extent of the littoral zone, and exposure to the sunlight connected to the position in the catchment.