Organic pollutants in industrial coastal basins are generated from a number of sources including coastal effluents and loading/unloading offshore stations. Such pollutants may adversely affect the quality intakes of other strategic coastal facilities such as coastal thermal desalination plants. In United Arab Emirates, many of such desalination plants are located along one coast hosting refineries as well as other coastal facilities. Loading and unloading of oil tankers are also practiced from offshore stations. A number of organic pollutants are generated from these sources and can potentially threaten the quality of intake seawater of the nearby desalination plants. This paper presents the results of a fate transport modeling study for two selected organic pollutants; Phenol and PCB-180 (HeptachloroBiphenyl) in an industrial coastal basin located in United Arab Emirates. A number of parameters involved in the transport processes were determined from lab experiments while most other parameters were estimated from a numerical sensitivity study. The model results depict contour maps of dissolved concentrations of the two considered pollutants for three different wind conditions in summer and winter. The obtained results and observations constitute useful information for the desalination plants' operators due to the effect of intake quality on the quality of final distillate produced from thermal desalination processes.