We investigated viral dynamics in the surface seawater at 13 stations in the western South China Sea (SCS) during the summer of 2007; 2 cold eddies formed during the sampling period. We found modest viral production and viral decay rates. Colloidal and heat-labile substances were important causes of viral removal (range 9.47 to 55.64% of viral production). During the sampling period, 26.44 to 96.08% (average 77.82%) of bacterial production was lysed by viruses, and a highly significant positive relationship was found between the rate of virus-induced bacterial mortality (m) and bacterial growth rate (mu). According to the hydrological conditions and station location, the 13 stations investigated in the SCS were further subdivided into 4 regions: Cold Eddy I (CE I), Cold Eddy II (CE II), oligotrophic oceanic water (OO water) and Mekong River plume (MR plume). Overall, viral activities appeared more dynamic in mesotrophic cold eddies and in the river plume than in oligo trophic SCS waters. However, a significantly lower bacterial growth rate, virus-induced bacterial mortality rate and m/mu, together with a high burst size in the MR plume compared to the CE I, CE II and the OO water, indicates that bacterial and viral activities have distinct responses to the upwelling of cold subsurface waters and the freshwater plume. Our results demonstrate that viral lysis is an important cause of loss of bacterial production in the SCS in summer, which may enhance CO(2) emission to the atmosphere by respiratory processes.