This research characterizes different wastewater treatment plant effluent nitrogen species in order to further understand the organic fraction of effluent nitrogen. Four effluents from biological nutrient removal (BNR) treatment and conventional activated sludge (CAS) treatment processes were investigated. Proteomic tools were applied in characterizing effluent protein. The protein profiles show the presence of active enzymes in all effluents and the organic nitrogen in the BNR effluent is more diverse than that in the CAS effluent, especially in the size range of 50-75 kDa. Size fractionation of the effluents suggests that over 70% of the effluent protein is soluble and most of the soluble proteins have a size smaller than 1kDa.