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Context We studied the virus component in the microbial food-web in the tropical coastal Sunda Shelf waters. Aims We investigated viral processes, including the lysogenic to lytic shift dynamics with seawater warming and nutrient enrichment. Methods We sampled nearshore and offshore waters of Peninsular Malaysia to provide a natural trophic gradient for correlational analyses. We also conducted laboratory experiments to investigate the changes in virus production rates and lysogeny, when temperature (range: 25–37°C) and nutrient concentrations (range: 0.1–1.0× marine-broth concentration) were manipulated. Key results Observations showed site-dependent differences in dissolved inorganic nutrient concentration, Chl-a (0.21–3.54 μg L−1) and bacterial abundance (4.09 × 105−9.41 × 105 cells mL−1), but not in viral abundance (measured as virus-like particles or VLP) (1.04 × 106−2.39 × 106 VLP mL−1) and virus production rates (0.59 × 105−4.55 × 105 VLP mL−1 h−1). From laboratory experiments, both warming and nutrient enrichment increased virus production (R2 > 0.651), decreased lysogeny (R2 > 0.743), and resulted in an increase of the viral lysis:bacterial production ratio, and a stronger viral control on bacterial production. Conclusions Although both seawater warming and nutrient enrichment increased virus production and reduced lysogeny, nutrient enrichment was a more important factor. Implications The increasing nutrient concentrations in these waters will increase virus production and virus top-down control of bacteria, and drive the ecosystem towards heterotrophy.