Lake water, pore water, and sediments were sampled in both polluted and unpolluted lakes from Southwestern (SW) China Plateau. The results show that although the mechanisms of nutrient regeneration were similar in the polluted and unpolluted lakes, the processes, however, were much stronger in the polluted lakes. Nitrogen regeneration was mainly of organic process. Phosphorus regeneration was essentially controlled by iron redox cycling near sediment/water interface. Nutrient upward fluxes were in the order SiO2 > NH4+ > PO4(3-). This study has significance for further investigating the response of nutrient biogeochemistry to the increasing nutrient levels in aquatic environments.