A new method to enhance nutrient removal from low carbon-wastewater was developed. The method consists of a two-sludge system (i.e., an anaerobic-anoxic-oxic reactor coupled to a nitrifying reactor (N-SBR)) and a nitrifying-sludge treatment unit using free nitrous acid (FNA). Initially, 65.1 +/- 2.9% in total nitrogen removal and 69.6 +/- 3.4% in phosphate removal were obtained without nitrite accumulation. When 1/16 of the nitrifying sludge was daily treated with FNA at 1.1 mg N/L for 24 h, similar to 28.5% of nitrite was accumulated in the NSBR, and total nitrogen and phosphate removal increased to 72.4 +/- 3.2% and 76.7 +/- 2.9%, respectively. About 67.8% of nitrite was accumulated at 1.9 mg N/L FNA, resulting in 82.9 +/- 3.8% in total nitrogen removal and 87.9 +/- 3.5% in phosphate removal. Fluorescence in-situ hybridization analysis showed that FNA treatment reduced the abundance of nitrite oxidizing bacteria (NOB), especially that of Nitrospira sp.