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Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and <i>Pseudomonas aeruginosa</i>, as well as 16S rRNA sequencing, to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites in Qatar. The concentration levels of indicator bacteria were affected by increasing temperatures and pH, and by decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that <i>Proteobacteria</i>, <i>Bacteroidetes</i>, and <i>Cyanobacteria</i> were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from <i>Flavobacteriaceae</i> (27.07%, 4.31%) and <i>Rhodobacteraceae</i> (22.51%, 9.86%) in seawater and sediment, respectively. <i>Alphaproteobacteria</i> (33.87%, 16.82%), <i>Flavobacteria</i> (30.68%, 5.84%), and <i>Gammaproteobacteria</i> (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, while <i>Clostridia</i> (13.72%) was abundant in sediment only. The results suggest that sediment can act as a reservoir for indicator bacteria, with higher diversity and lower abundance compared to seawater.