Abstract Viruses are active members of the microbial community in natural waters but little is known about the factors that regulate their activity and production. In this study we have investigated the effects of increased availability of organic nutrients and inorganic phosphate on activity, elemental composition, community structure and virus production in a natural bacterial community. The fraction of active cells in the community as estimated from microautoradiography of cells assimilating 3H-labeled thymidine ranged from 0–22%, but changes in the elemental composition of the cells indicated that more than 90% of the cells were active. The increase in carbon and energy availability stimulated virus production more than bacterial biomass production, while the increase in phosphate availability stimulated biomass production rather than virus production. A decrease in morphological diversity of the bacterial community was paralleled by a reduction in the virus-to-bacteria ratio (VBR) but the relationship between bacterial diversity and viral activity is uncertain. Our general conclusion is that nutrient availability, in addition to the bacterial activity, also affects the viral activity, and that both of these may affect the structure and diversity of the bacterial community.