The carbon-flux via algal bloom events involves bacteria as an important mediator. The present study, carried out during the spring inter-monsoon month of April 2008 onboard CRV Sagar Manjusha-06 in the Eastern Arabian Sea, addresses the bloom-specific flow of carbon to bacteria via chromophoric dissolved organic matter (CDOM). Eleven stations monitored were located in the coastal, shelf and open-ocean areas off Ratnagiri (16°59′N, 73°17′E), Goa (15°30′N, 73°48′E) and Bhatkal (13°58′N, 74°33′E) coasts. Visible bloom of “saw-dust” color in the Ratnagiri shelf were microscopically examined and the presence of cyanobacteria Trichodesmium erythraeum and T. thieabautii with cell concentrations as high as 3.05 × 106 trichomes L−1 was recorded. Total bacterial counts (TBC) varied between 94.09 × 108 cells L−1 in the bloom to 1.34 × 108 cells L−1 in the non-bloom area. Chromophoric dissolved organic matter (CDOM) concentrations averaged 2.27 ± 3.02 m−1 (absorption coefficient 325 nm) in the bloom to 0.28 ± 0.07 m−1 in the non-bloom waters respectively. CDOM composition varied from a higher molecular size with lower aromaticity in the bloom to lower molecular size and increased aromaticity in the non-bloom areas respectively. Strong positive relationship of TBC with Chlorophyll a (R2 = 0.65, p < 0.01) and CDOM concentrations (R2 = 0.8373, p = 0.01) in the bloom area indicated hydrolysis and/or uptake of CDOM by bacteria. Absorption by mycosporine-like amino acid palythene (λmax = 360 nm) was recorded in the filtrate of bloom. Morphotypes of Trichodesmium-associated bacteria revealed a higher frequency of Gram-positive rods. The role of bacteria in relation to changing CDOM nature and as a factor in affecting oxygen content of the water column is discussed in context of the Arabian Sea.