Background and aims <p>Silicon (Si) bio–availability in soil is a critical constraint on the yield of Si–accumulating crops, especially as precipitation in arid and semi–arid areas is becoming high variability with climate change. This study aims to investigate how contrasting crop rotational pattern regulate plant–soil–water interactions that govern processes of soil–plant Si cycling.</p> Methods <p>This study investigated five typical crop cultivation patterns in the northern Loess Plateau and natural grasslands as the control. We collected their soil profile samples (0–50&#xa0;cm depth) including plant organs and dry matter yield. The contents of soil water were calculated through oven–drying method and plant available Si using 0.01&#xa0;M CaCl₂ extract. Additional analyses included contents of Si and phytoliths in plant organs.</p> Results <p>Analytical results presented that crop rotation significantly increased the storage of soil water (10.81–23.17&#xa0;mm, <i>p</i> &lt; 0.01) relative to long–term grassland (2.55–13.21&#xa0;mm), and millet–soybean rotation demonstrated the highest increase of soil water storage. In contrast, grassland retained high content of plant available Si (33.8–49.0&#xa0;mg&#xa0;kg⁻¹), which was about 1.4 times as that of the crop rotations. We further found that maize–millet rotation pattern resulted in the greatest depletion of plant available Si storage _{0–50&#xa0;cm} (122.8&#xa0;kg Si ha⁻¹) and a large amount of Si uptake (phytolith accumulation 134.0–236.5&#xa0;kg&#xa0;ha⁻¹&#xa0;yr⁻¹).</p> Conclusion <p>Our findings indicate that crop rotation significantly accelerate the depletion of plant available Si in the soils. This might be attributed to increased crops Si uptake, thus enhancing Si biological cycling in soil–plant system.</p>