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A study was carried out in the sea adjacent to a major MSF plant where a new 24MGD SWRO plant is being commissioned. Data were collected on the topographical feature of the marine basin, water quality and plankton of the intake zone. The incidents of planktonic bloom, influx of invasive organisms like jellyfish and macrofouling organisms and ingress of marine algae were monitored regularly. The Intake Bay of the plant is a well designed man-made structure studded to the coast. The marine basin in Al-Jubail, is for geological reasons, a shallow gently sloping shelf while the bay proper is a dredged, deeper basin. The area outside the bay is a vast sea grass bed and the seafloor sediment is sandy. The drag of seawater maintained by the intake pumps facilitates the transport of sediment particles, uprooted algae and floating objects creating fouling problems inside the plant. Seawater temperatures, conductivity, pH, dissolved oxygen and trace metals were found to be very much benign to the trouble free operation of the plant. Influx of jellyfish, noticed during the summer, was not found to be very severe. Data on plankton showed the presence of many phyto and zooplankton organism of biofouling potential in the plant. Total suspended solids indicated the possibility of the intake bay becoming a source of elevated Silt Density Index (SDI) for the new SWRO plant. The paper considers the data in detail and discusses the effects of environment on the desalination plant in Al-Jubail and suggests certain strategies for the protection of seawater intakes and some points useful in the siting and design of coastal seawater intakes in the region.