<p>Viruses are increasingly recognized as key components of microbial food webs, influencing planktonic community structure and carbon cycling in marine ecosystems; however, their role in subtropical coastal systems of the Gulf of California remains poorly understood. In this study, we examined the seasonal dynamics of virioplankton and their potential influence on the size structure of bacterioplankton and phytoplankton in a meso-eutrophic coastal lagoon. Virioplankton abundances ranged from 2.0 to 16.3 × 10⁷ VLP&#xa0;ml⁻¹ (mean: 7.0 × 10⁷), while bacterioplankton abundances varied from 3.8 to 16.5 × 10⁶ cells ml⁻¹ (mean: 8.7 × 10⁶ cells ml⁻¹). Spatiotemporal patterns in virioplankton abundance and virus-to-host ratios showed pronounced increases during winter–spring, coinciding with elevated dissolved inorganic nitrogen concentrations and higher phytoplankton biomass associated with seasonal runoff and coastal upwelling. Under these conditions, increased virus-to-host ratios suggest enhanced viral–host interactions during periods of high microbial activity. A significant positive association between virioplankton and bacterioplankton abundances (<i>p</i> &lt; 0.05) supports a close coupling between viruses and prokaryotic hosts. Partial redundancy analysis identified dissolved oxygen as the strongest environmental predictor of virus-to-host ratios. In contrast, negative associations with temperature and urea may indicate reduced viral replication efficiency or a greater prevalence of non-lytic infection strategies under warmer, nitrogen-limited conditions. These findings underscore the context-dependent nature of virus–host interactions and stress the need to quantify and integrate viral processes into conceptual and biogeochemical models of coastal ecosystems shaped by anthropogenic nutrient inputs.</p>