Total nitrogen (TN) and total phosphorus (TP) concentrations are important parameters to assess the quality of water bodies and are used as criteria to regulate the water quality of the effluent from a wastewater treatment plant (WWTP) in Korea. Therefore, continuous monitoring of TN and TP using in situ instruments is conducted nationwide in Korea. However, most in situ instruments in the market are expensive and require a time-consuming sample pretreatment step, which hinders the widespread use of in situ TN and TP monitoring. In this study, therefore, software sensors based on multiple-regression with a few easily in situ measurable water quality parameters were applied to estimate the TN and TP concentrations in a stream, a lake, combined sewer overflows (CSOs), and WWTP effluent. In general, the developed software sensors predicted TN and TP concentrations of the WWTP effluent and CSOs reasonably well. However, they showed relatively lower predictability for TN and TP concentrations of stream and lake waters, possibly because the water quality of stream and lake waters is more variable than that of WWTP effluent or CSOs.