It is generally considered that nitrogen is one of the major factors regulating the trophic status of lakes, and the biogeochemical cycling of nitrogen serves the most important function in lake systems. Lakes often receive large anthropogenic inputs of nitrogen that cause eutrophication, and the exchange of nitrogen-compounds between sediment and water has a profound effect in all kinds of lakes. Such increased nutrient loading promotes the growth of phytoplankton while rooted plants and benthic are suppressed due to reduced light availability, the transfer of the nitrogen through the food chains in algal lake and macrophytic lake is different accordingly. Meanwhile, in this review progresses made on the processes such as nitrification, denilrification, nitrogen fixation and anammox (anaerobic ammonium oxidation) are emphasized. Methods and techniques applied in the research of biogeochemical cycling of nitrogen are also summarized, and the development of molecular techniques has contributed enormously to the rapid recent progress in the field. Current insufficiencies are pointed out and future directions are recommended in the end.