Vertical and temporal distributions of N and P in soil solution in aquatic-terrestrial ecotone (ATE) of Taihu Lake were investigated, and the relations among N, P, ORP, TOC, root system biomass and microorganism were studied. As a whole, significant declines in TN, NO3-N, DON and TP concentration in soil solution have occurred with increase of the depth, and reached their minima at 60 cm depth, except for NH4+-N, which increased with depth. the concentration of TP increased gradually from spring to winter in the topsoil, the maximum 0.08 mg/L presented in the winter while the minimum 0.03 mg/L in spring. In the deeper layer, the concentration value of TP fluctuated little. As for the NO3-N, its seasonal variation is significant at 20 cm depth, its concentration increased gradually from spring to autumn, and decreased markedly in winter. Vertical and temporal distribution of DON is contrary to that of NO3-N. The results also show that the variation of N and P in the percolate between adjacent layers is obviously different. The vertical variation of TN, TP, NO3-N, NH4+-N and DON is significant, of which the variation coefficient of NO3-N along the depth reaches 100.23%, the highest; while the variation coefficient of DON is 41.14%, the smallest. The results of correlation analysis show that the concentration of nitrogen and phosphorus correlate significantly with TOC, ORP, root biomass and counts of nitrifying bacteria. Most nutrients altered much from 20 to 40 cm along the depth. However, DON changed the more between 60 and 80 cm. Results show that soil of 0-60 cm depth is active rhizoplane, with strong capability to remove the nitrogen and phosphorus in ATE. It may suggest that there exists the optimum ecological efficiency in the depth of above 60cm in reed wetland. This will be very significant for ecological restoration and reestablishment.