<p>The Biogeochemical cycles are crucial for aquatic ecosystems, particularly the functioning of nutrient cycles. Growing anthropogenic pressure alters their functioning, causing accelerated eutrophication. Understanding the scale of alteration in ecological functions could assist with combat strategies. Bacterial communities regulate the transition of functional traits in aquatic ecosystems. However, current knowledge is still elusive regarding the variability of the environmental drivers dictating the functional roles in dynamic regimes like littoral zones. This study assessed how seasonal and circumlimnal conditions influenced sediment characteristics, bacterioplankton communities, and putative ecological functions (specifically biogeochemical cycling of carbon, nitrogen, and sulphur) in the hypertrophic freshwater Lake Pichola (Rajasthan, India). Findings suggest a significant seasonal drivers’ influence on sediment characteristics, while the anthropopressure-aided niche partitioning promoted species richness and diversity in the hypertrophic lake. Proteobacteria, Bacteroidota, and Firmicutes were abundant phyla; chemoheterotrophy and fermentation are the dominant potential putative functions; methylotrophy, nitrate reduction, and sulfate reduction are prominent nutrient cycling biogeochemical functions. Redundancy analysis accurately explained the influence of sediment characteristics on the variability of biogeochemical functions. Shifts in bacterioplankton communities were evident within circumlimnal regimes with greater anthropogenic stress, promoting higher abundance and diversity of putative bacteria orchestrating the ecological functions. This study emphasizes the importance of considering the interplay among the functional traits and environmental factors dynamics in littoral sediments for studying biogeochemical transformation in lakes.</p>