Viruses are known to be important agents of prokaryotic loss in diverse environments. However, only few studies to date have examined seasonal variations in virus-prokaryote interactions in marine environments. This study measured viral and prokaryotic abundance between January and November, 2015 to assess seasonal variations in the relation between viruses and prokaryotes (heterotrophic bacteria, Synechococcus spp. and picoeukaryotes) in eutrophic semi-enclosed and less productivity open coastal waters. Viruses and prokaryotes were found to be significantly more abundant in productive semi-enclosed coastal waters. Using side scatter and green DNA dye complex fluorescence, we analyze flow cytometry (FCM) data to clearly distinguish between two groups of viruses, VLP1 and VLP2. VLP1, the most dominant, ranged from 84% to 89% and 67% to 78% in semi-enclosed and open coastal waters, respectively. Lower virus-to-bacteria ratios (VBR) were observed at semi-enclosed coastal waters (0.9 to 6.1), due to turbidity values of these two coastal waters being significantly different (4.5-6.2 NTU and 0.5-1.2 NTU, respectively) in summer, probably a result of higher suspended matter causing removal of viruses from the surface waters.