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The Saudi Arabian Saline Water Conversion Corporation (SWCC) aims to maintain an uninterrupted desalinated water output and has tasked its Desalination Technologies Research Institute (DTRI) with trouble-shooting operational problems and unusual events faced by its desalination plants. Three events were reported and investigated by DTRI. Two were found to involve fungal fouling, and one was found to involve fouling by marine shells. One case of fungal fouling involved a new seawater reverse osmosis membrane and the plant was advised to review the handling and storage practice of membranes. The other case involved product water hoses and manifested itself in the form of black slimy deposits arising from dense fungal growth. The fungus originated from new product hoses and was eliminated by shock-dosing replacement hoses with chlorine. The marine shell fouling involved a feed water line of a combined power/desalination plant. Chlorine, hydrochloric acid, ethylenediaminetetraacetic acid, and fresh water were used to assess their ability to control marine shell fouling in laboratory experiments, with varying results. Since high doses of chlorine were not effective in controlling marine shell fouling, the practice of continuous chlorination should be abandoned in favor of an alternative chlorination regimen, e.g., pulse chlorination.