Mitigation of anthropogenic climate interference will likely require the removal of legacy atmospheric carbon dioxide (CO2). Ocean alkalinity enhancement (OAE) is an abiotic marine carbon dioxide removal (mCDR) approach that accelerates the natural Earth process of rock weathering, but its effects on marine ecosystems remain uncertain. Here we used outdoor mesocosm experiments to investigate the effects of abrupt limestone-inspired and NaOH alkalinity additions of ~750 μmol kg-1, reflecting model-predicted OAE scenarios that produce severe localized impacts (e.g., large variations in pH and Ω). We assess the response of seasonal marine microbial communities (phytoplankton, bacteria) and viruses from the Santa Barbara Channel, analyzed by high-throughput amplicon sequencing and flow cytometry. Alkalinization, particularly under low-nutrient conditions, altered microbial diversity and promoted the proliferation of parasites (Syndiniales), suggesting that abrupt alkalinization could alter marine ecosystem composition, and potentially its function, near coastal alkalinity deployment “hotspots”. We highlight the need for rigorous environmental risk assessments prior to implementation of OAE technologies.