Size fractionation was performed using water from the Great Reef of Toliara (Madagascar) taken from two different habitats (ocean and lagoon) during the dry and wet seasons, to study the growth and mortality rates of bacterioplankton. Experiments were conducted with 1 and 100% of heterotrophic nanoflagellate (HNF) concentrations and virus-free water was obtained by tangential filtration (10 kDa). During the dry season, in both environments, bacterial abundance and production were significantly lower than values recorded during the wet season. Bacterial growth rates without grazers were 0.88 day–1 in the lagoon and 0.58 day–1 in the ocean. However, growth rates were statistically higher without grazers and viruses (1.58 day–1 and 1.27 day–1). An estimate of virus-induced bacterial mortality revealed the important role played by viruses in the lagoon (0.70 day–1) and the ocean (0.69 day–1). During the wet season, bacterial growth rates without grazers were significantly higher in both environments than were values obtained in the dry season. However, the bacterial growth rates were paradoxally lower in the absence of viruses than with viruses in both environments. Our results suggest that changes in nutrient concentrations can play an important role in the balance between viral lysis and HNF grazing in the bacterial mortality. However, virus-mediated bacterial mortality is likely to act simultaneously with nanoflagellates pressure in their effects on bacterial communities.