Significance Despite years of research in aquatic virology, we remain unable to estimate viral-induced mortality in the ocean and, consequently, to resolve viral impact on nutrient fluxes and microbial dynamics. Here, we assess active infection in algal single cells by subcellular visualization of virus and host transcripts, revealing the coexistence of infected and noninfected subpopulations. We revisit major assumptions of a giant virus’ life cycle: cells can produce virions without lysing and can lyse without producing virions. In a natural algal bloom, only 25% of cells were infected, highlighting the importance of other mortality agents. Enrichment of infected cells in cell aggregates suggests potential host defense strategies. Our approach opens a mechanistic dimension to the study of marine microbial interactions.