Silicon (Si) and its biogeochemical cycling play an important role in maintaining the functions of terrestrial and marine ecosystems. However, the effects of sea level rise on the biogeochemical cycling of Si in coastal wetlands remain poorly understood. To explore this impact on biogeochemical Si cycling, we sampled a gradient from sediment to soil without the impact of tidal inundation in the Beidagang Wetland Nature Reserve, and then assayed non-crystalline Si (labile Si), including mobile Si (CaCl2-Si), adsorbed Si (Acetic-Si), Si bound to soil organic matter (H2O2-Si), Si occluded in pedogenic oxides/hydroxide (Oxalate-Si), and amorphous Si (Na2CO3-Si) fractions. Analytical results showed that the content of CaCl2-Si ranged from 13.0 to 53.3 mg kg−1 and the content of Acetic-Si ranged from 32.3 to 80.9 mg kg−1, both of which were lower in sediments compared to soils. The content of H2O2-Si (84.1–160.1 mg kg−1) and Oxalate-Si (306.6–655.1 mg kg−1) in the soil profiles showed non-significant variations along the sampling slope. The Na2CO3-Si fraction accounted for 82%–90% of labile Si in soil and sediment, mainly being contributed from phytoliths or diatoms. Diatoms were only detected in sediment profiles. The storage of labile Si in sediment was significantly (p = 0.0009) lower than the storage in soil, suggesting that the coastal wetland ecosystems are an important source of Si to the estuary. With future sea level rise and increased margin erosion, the inter-transformation processes among different Si fractions would likely be weakened to increase dissolved Si for marine diatoms.