The present study investigated the prevailing condition of water quality with surface water movement in relation to the existing bridges across the Batticaloa lagoon,Sri Lanka. Kottamunai and Puthupaalam bridges and associated roads not only act as barrier to prevent the mixing of lagoon water but also they change physio chemical parameters by concentrating the pollutants in surface waters. Physio chemical biological parameters of salinity, turbidity, surface water velocity, density, temperature, dissolved oxygen, nitrite, nitrate, pH, phosphate, plankton and fish abundance were measured routinely at approximately a week interval for six months from 2nd July 2008 to 22nd December 2008 over the wet and dry seasons on either sides of Kallady, Kottamunai and Puthupaalam bridges. The existing conditions were found to have strong impact on salinity, temperature, surface velocity, turbidity, dissolved oxygen, nitrite, pH and also on fish migration and plankton assemblages. The trends in these parameters were largely determined by surface water flow and lagoon geomorphology.