Arid countries around the world, particularly in the middle East and North Africa (MENA) region rely heavily on seawater desalination process to produce fresh water. The rapid increase in the construction of reverse osmosis (SWRO) desalination plants near coastal areas, has been accompanied with the expansion of Harmful Algal Blooms (HABs). Problems associated with HABs had created continuous challenges to SWRO desalination plants. In this study, the influence of the physical-chemical and biological factors on phytoplankton community structure and on HABs forming algae was investigated in the Northwest of the Sea of Oman near Majis desalination plant (Sohar Industrial Port, SIP) from April, 2018 to March, 2019. This is the first study carried out in the coastal waters of Oman aimed to examine the presence of HABs forming algae and their cysts near the desalination plant located in industrial area. 144 seawater samples were collected in a weekly basis at three stations (Out, Intake, and Outfall) from one sampling point per station. A total of 64 phytoplankton taxa were recorded during this study, in which each station exhibited different phytoplankton composition in terms of presence and abundance of taxa through the study period. Bacillariophyceae (Diatoms) were the dominant phytoplankton groups at all stations and contributed with the highest number of taxa. Station "Out" was reported the highest number of diatom species (42 species), while "Outfall" station was reported the lowest number of diatom species (28 species). The second most abundant phytoplankton group was Dinophyceae (Dinoflagellates), in which the highest number of species were reported at station "Out" (21 species), while the lowest number of species were reported at station "Outfall" (11 species). Only one cyanobacterium species "Trichodesmium erythraeum" was found. This species was dominant at station ''Outfall'' through-out the year and reached the maximum abundance (97780 cell/ L) during Spring Inter-Monsoon (SIM). In total, 20 HABs species were recorded. Pseudo-Nitzschia spp., Chaetoceros spp., Coscinodiscus sp. Ceratium spp., Dinophysis spp., Prorocentrum gracile, and Gyrodinium spirale, were the most common HABs species that appeared through-out the year at Majis Industrial Services Company (MISC) facility area. Noctiluca scintillans, Margalefidinium polykrikoides, Protoperidinium spp., Scripsiella sp., Alexandrium sp., Gonyaulax sp., and Trychodesmium erythraeum, appeared only in specific season(s). Some of these HABs species reported were potential toxic species. The highest number of cell counts was recorded in winter season, especially during the Northeast Monsoon (NEM) and Fall-Inter Monsoon (FIM), while the lowest number of cell counts was recorded during spring and summer, except at the end of summer during Southwest Monsoon (SWM), particularly in September. Most physico- chemical properties of surface water exhibited seasonal and spatial variations. The localized nutrients enrichment of nitrate (NO3), ammonium (NH3), silicate (SiO4) and the changes in seawater temperature were the most important factors that controlled the seasonal fluctuations of phytoplankton (HABs) during the study period at MISC facility area. These factors were the main ones responsible for the frequent HABs occurrence in the area. Cysts of seven HAB forming dinoflagellates were found at Sohar Industrial Port (SIP) area. Most of them dominated by potentially toxic dinoflagellates species. This finding revealed that SIP provides suitable environmental conditions for HAB cysts-forming algae. The study indicated that nitrogen containing chemicals from the industrial companies, which MISC supply with water, could have an impact on the abundance and diversity of phytoplankton communities around the desalination plant particularly at ''Outfall'' station. One of the most important recommendations of the study is to continue monitoring the physical-chemical and biological changes of the seawater and the presence of HABs species and their cysts not only near the MISC area but also in SIP.