Silicon (Si) is an essential nutrient for many plants as well as an important element that controls the functions of terrestrial and aquatic ecosystems. Wetland ecosystems are considered to be very important for Si transport and transformation in nutrient biogeochemical cycles. However, information on Si cycling in wetland ecosystems is scarce. The Shanyutan wetland is the largest tidal wetland in the estuary of the Min River, southeast China. In this study, the Si distribution pattern and its influencing factors were determined by seasonally measuring the levels of dissolved silicates (DSis) in the porewater and biogenic silica (BSi) in the sediments of Phragmites australis wetland (PAW), Cyperus malaccensis wetland (CMW), and Spartina alterniflora wetland (SAW) from October 2012 to September 2013. For better comparison, three sampling sites were added in SAW since January 2013; these sites were isolated by a 30m wide tidal creek. The sampling sites near the land were marked as S. alterniflora wetland (inside; SAWI), whereas those near the sea were marked as S. alterniflora wetland (outside; SAWO). The results indicated that the average contents of BSi were 14.33 mg/g in SAWO, 10.40 mg/g in CMW, 9.98 mg/g in PAW, and 7.50 mg/g in SAWI. The average concentrations of DSis in the sediment porewater were 407 μmol/L in SAWO, 359 μmol/L in SAWI, 344 μmol/L in CMW, and 323 μmol/L in PAW. Generally, the contents of BSi in the sediments and DSis in the porewater were higher in summer and autumn, whereas they were lower in spring and winter. Statistical analysis revealed significantly positive correlations between DSi concentration in the porewater and BSi content in the sediments or the distance from the shoreside to the tidal creek (P<0.05). BSi content in the sediments was slightly positively correlated with temperature. Taken together, our findings suggest that the distribution of Si in the wetlands of the Min River estuary was correlated with vegetation, temperature, and tidal action. Unlike that of native species, the invasion of S. alterniflora, to some extent, altered the distribution patterns of Si in the wetlands.