In the seawater desalination inorganic constituents (40,000-50,000 ppm) pose serious problems to multistage flash (MSF) process and more acutely to seawater reverse osmosis (SWRO) process which is also greatly influenced by organic content of (2-4 ppm). It is well-known that fouling on the RO membrane causes serious problems including (i) gradual decline of membrane flux thereby decreasing permeate production, (ii) an increase in DeltaP thereby increasing the requirement of high pressure pump rating and (iii) degradation of membrane itself. The dissolved organic matter is not a single substance but a mixture of ill-defined aliphatic and aromatic compounds. Humic substance constitute major portion of total organics in seawater, thus to identify the nature, and compositional characteristic of such substance along with its estimation is of utmost importance to overcome the problems associated with fouling of RO membranes. Humic substances from Al-Jubail, Al-Khobar (Gulf Coast) and Jeddah (Red Sea Coast) were isolated and analyzed by different techniques, viz elemental analysis, W-visible spectrometry, IR Spectrometry and fluorescence spectrometry. Method of isolation and purification of humic substance has been standardized to recover gram quantities. Two methods of quantitative estimation have also been developed. The first method involves estimation of humic substance from seawater by W-visible spectrometer after isolation. In the second method, humic substance was determined using fluorescence technique by spectro-photofluorometer either after isolation and pre-concentration or directly in the seawater without isolation. The precision of methods in terms of percentage relative standard deviation for UV-visible method is 3.8% while for fluorescence method is 1.75%. Elemental composition, nature, IR spectra and concentration of humic substances of Al-Jubail and Al-Khobar are similar. However, humic substances from Jeddah differed in many respects including the composition. The remarkable deviation in elemental composition indicates that perhaps nature and origin of humic substances from Gulf and Red Sea coasts are different. High nitrogen, sulphur and hydrogen to carbon ratio indicate high bacterial activity in the Red Sea region.