The fate of soil biogenic silica (BSi) in coastal salt marshes is of global importance because of its role in providing both available silicon (Si) for the growth of plants and diatoms and in sequestering carbon (C) (blue C) in soils and sediments. However, the accumulation of BSi and BSi-occluded C (BSiOC) under different vegetation habitats in coastal ecosystems, particularly in response to relative sea‐level rise (RSLR), remains poorly understood. Here we established a paired waterlogging-control system and collected the soil samples under both waterlogged and non-waterlogged conditions from three vegetation habitats (single Phragmites australis, a mixture of P. australis and Suaeda salsa, and single S. salsa) corresponding to a gradient of distance from the coastline in three independent salt marshes. Our findings indicated that RSLR decreased average BSi content, especially in the 0–20 cm soil layer of the single P. australis and the mixed P. australis and S. salsa community. Although RSLR increased soil organic C (SOC) content, it generally decreased soil BSiOC content and its contribution to SOC. Consequently, RSLR resulted in lower soil BSi and BSiOC densities, particularly in the salt marsh dominated by the Si accumulator P. australis. Here, BSi and BSiOC densities at depths of 0–80 cm decreased by an average of 19% and 18% following waterlogging, respectively. The BSi pool was dominated by phytoliths in non-waterlogged soils, while both diatoms and phytoliths were present in soils subjected to RSLR. Soil physicochemical properties including SOC, electrical conductivity and dissolved Si were influenced by RSLR. These factors, along with erosion were suggested as key influencers for BSi and its C sequestration in coastal salt marshes. Our results provide a scientific basis for elucidating biogeochemical Si cycles and predicting changes in BSiOC sequestration to optimize its storage.