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Background and aims: Silicon (Si) deficiency is a major constraint on rice production. The objective of this study was to evaluate the long-term influence of phytolith-rich straw return and groundwater table management on labile Si fractions in paddy soil and subsequent plant Si uptake. Methods: A field experiment was conducted over 36 years in subtropical China with different application doses of phytolith-rich straw and a groundwater table of either 20 or 80 cm. An optimized sequential chemical extraction procedure allowed us to determine labile Si fractions, represented by CaCl2-Si, Acetic-Si, H2O2-Si, Oxalate-Si, and Na2CO3-Si. Additional analyses included the determination of amorphous silica particles in soil, phytoliths in supplied straw, Si in planted rice straw, and the dissolution rate of phytoliths extracted from supplied straw. Results: Long-term application of phytolith-rich straw significantly increased the H2O2-Si and Na2CO3-Si contents. The CaCl2-Si (5.21–7.91 mg kg− 1), H2O2-Si (50.0–72.4 mg kg− 1) and Na2CO3-Si (3.33–4.60 g kg− 1) contents were positively correlated with soil organic carbon. The Si content (13.6–28.9 g kg−‍1) in planted rice straw significantly (p < 0.05) increased with the application dose of phytolith-rich straw under both groundwater tables. This effect was significantly (p < 0.05) greater under 80 cm groundwater table than under 20 cm groundwater table for matching straw amendments. Conclusions: This study indicates that long-term application of phytolith-rich straw and groundwater management significantly increase soil Si bioavailability by promoting accumulation of organic matter and phytoliths, and enhancing the soil-plant Si cycle. [ABSTRACT FROM AUTHOR]