Cracks are common and natural features of sea ice formed in the polar oceans. In this study, a sea ice crack in flooded, multiyear, land‐fast Antarctic sea ice was examined to assess its influence on biological productivity and the transport of nutrients and microalgae into the upper layers of neighboring sea ice. The water inside the crack and the surrounding host ice were characterized by a strong discoloration (brown color), an indicator of a massive algal bloom. Salinity and oxygen isotopic ratio measurements indicated that 64–84% of the crack water consisted of snow meltwater supplied during the melt season. Measurements of nutrient and chlorophyll a concentrations within the slush layer pool (the flooded layer at the snow‐ice interface) revealed the intrusion of water from the crack, likely forced by mixing with underlying seawater during the tidal cycle. Our results suggest that sea ice crack formation provides conditions favorable for algal blooms by directly exposing the crack water to sunlight and supplying nutrients from the under‐ice water. Subsequently, constituents of the crack water modified by biological activity were transported into the upper layer of the flooded sea ice. They were then preserved in the multiyear ice column formed by upward growth of sea ice caused by snow ice formation in areas of significant snow accumulation.