Monthly research of ammonia and phosphorus fluxes in water-sediment interface in East Lake Taihu (ELT, macrophyte dominated) and Meiliang Bay (MB, algae dominated) was processed with intact sediment cores' incubation and pore water diffusive model. The ammonia and phosphorus fluxes calculated with intact sediment cores' incubation (F(i)) showed discrepancy in different lake zones with different ecotype. The yearly average fluxes of ammonia and dissolved phosphorus in ELT were (44.9 +/- 21.9) mg x (m2 x d)(-1) (Mean +/- SD) and (2.06 +/- 1.71) mg x (m2 x d)(-1); and (16.2 +/- 12.0) mg x (m2 x d)(-1) and (0.53 +/- 0.52) mg x (m2 x d)(-1) in MB. The molecular diffusive fluxes (F(m)) of the two lake zones showed the same pattern, but the absolute value difference may as high as an order of magnitudes. So this molecular diffusive model cannot be used to evaluate the nutrients fluxes in sediment-water interface in Lake Taihu, a lake vulnerable with wind and wave affection and benthic bio-disturbation. Compared with the two lake zones with different ecotypes, macrophyte dominated one had higher nutrients fluxes than the algae one. ELT had higher bio-disturbation, which was revealed by the F(i)/F(m) ratio. When the dissolved oxygen (DO) remained in high concentration, known as aerobic condition, the nutrients' fluxes were not correlated with the DO. Similarly, the fluxes were not correlated with the nutrients' concentration of the overlying water at the existing condition. The discrepancy between higher nutrients' fluxes and lower nutrients loading in ELT suggested the higher particulate settlement rate and assimilate rate promoted by the macrophyte. This is the important theoretical basis of rebuilding the healthy ecosystems with restoring the water plants.