High water quality is essential for aquatic life and human beings. The microbial communities are the major component of the river ecosystem. However, the microbial communities of the river water ecosystems are susceptible to changing climatic and other environmental factors, for instance, water pH, temperature, nutrient contents, and concentrations of metals and minerals. So, there is a need to understand the composition and diversity of water-inhabiting microbial communities concerning the water chemistry in different seasons. This study aims to determine the impact of seasonal variations on the microbial communities in the Alabama River. We hypothesize that microbial communities and their interactions with the water chemistry will change across seasons. Thus, it can also help us understand the changes in microbiology of the Alabama River concerning changing conditions. For the molecular analysis, we sampled the Alabama River water at the Montgomery downtown site bi-weekly to study changes in water properties and microbial communities. We have observed changes in water properties while processing our samples for next-generation sequencing of microbial communities to profile the composition and diversity of taxa. This study will help us understand the functional features of the microbial community as a function of seasonal climatic variations and water properties.