Hydrodynamics are the key factor influencing sediment resuspension, transport and nutrient release in large shallow lakes. However, the hydrodynamic responses of bottom traps during pollutant capture remain unclear. In this study, a large eutrophic shallow lake was selected to carry out a field test of deep traps at the lake bottom. Based on observations of the lake current around the trap, the sedimentation rate of the particles in the trap and the nutrient content of the captured sediments, combined with the numerical simulation of the waves outside the trap, the effects of lake currents and waves on the sediment deposition in the traps were studied, and the response of the nutrient content of the sediments captured in the deep traps to the changes in lake currents and waves was analyzed. The results showed that the strong hydrodynamic force significantly promoted sediment deposition in the trap and enhanced the ability of the trap to capture sediments with high nutrient contents. The influences of waves and lake currents on the bottom trap capture of polluted sediments varied among different periods. Waves played the leading role in winter and spring, accelerating sediment capture in the bottom traps near the southern shore of eastern Lake Chaohu during this period. In summer, the lake current was the main dynamic factor contributing to the rapid deposition of particulate matter and the capture of sediments with high nutrient contents in the bottom traps of western Lake Chaohu. The multiple stepwise linear regression model based on lake current and wave data explained 37.6 % of the sediment deposition in the trap, and the model built for a single bottom trap explained more than 80 % of the deposition. After correcting the sediment deposition thickness in the trap by considering the water content of the sediment, the quantitative relation yield better inversion results for the sediment deposition process, and different thicknesses in the bottom trap were linked to different sediment deposition periods. According to the hydrodynamic strength in 2020, the thickness of the highly contaminated sediments captured by traps CC1-CC5 was calculated to be 1.09–1.93 m, and the corresponding TN and TP were 26.66–68.53 kg and 6.84–19.89 kg, respectively. This study provides a scientific analysis and guidance for the evaluation of endogenous nutrients captured by lake bottom trap methods.