The spatial distribution of bacterial communities inhabiting sediment is heterogeneous at different spatial scales, but mostly unexplored. Here, it is postulated that the heterogeneity of the bacterial community composition varies at the same scale of the heterogeneity of sediment chemical properties. The large spatial scale (km) diversity in sediment from a brackish water lagoon (Chilika Lake, India) is studied, considering the large scale physical and chemical characteristics of land cover, climate, pH, and salinity. Seventy-two samples (24 stations, 3 seasons: winter, rainy, and summer) of sediment from Chilika Lake were analyzed by 16S ribosomal ribonucleic acid (rRNA) gene sequencing, and the relations with land cover and other physico-chemical parameters are discussed. More samples were collected after a severe cyclonic storm (Phailin) passed near the lagoon in 2013, to see the impact of the tropical storm on the spatial and temporal distribution of bacteria in the sediment. The results demonstrate clear spatial relations between physico-chemical parameters (e.g., salinity), land surfaces (e.g., drainage area), and the distribution of sediment microbial communities.