Little information is available on the influence of substantial precipitation and particulate matter entering during the monsoon process on the release of potentially toxic elements (PTEs) into lake sediments. Sediments from a typical subtropical lake across three periods, pre-monsoon, monsoon, and post-monsoon, were collected to determine the chemical forms of 12 PTEs (As, Cd, Co, Cr, Cu, Fe, Hg, Pb, Mn, Ni, Sb, and Zn), magnetic properties, and physicochemical indicators. Feature importance, Shapley additive explanations, and partial dependence plots were used to explore the factors influencing bioavailable PTEs. The proportion of bioavailable forms of PTEs decreased from 3.85 % (Cd) to 87.84 % (Hg) after the monsoon. Gradient extreme boosting demonstrated robust fitting accuracy for the prediction of the bioavailable forms of the 12 PTEs (R2 > 0.84). Shapley additive explanations identified that the bioavailable forms were influenced by the total PTE concentrations, wind, shortwave radiation, and particle inputs (25.1 %–88.5 % for total importance), either individually or in combination. The partial dependence plots highlighted the influence thresholds of background values and anthropogenic factors on the bioavailable forms of PTEs. Changes in environmental properties could indicate the process of external sediment influx into lakes. The optimized model combined with magnetic parameters showed strong performance in other cases (coefficient of determination>0.58), confirming the ubiquitous decrease in bioavailable forms of PTEs in sediments across subtropical lakes after monsoons.