Urmia Lake in the northwestern of Iran is a hypersaline water body and has become an environmentally important issue especially due to the presence of an infrequent aquatic species, Artemia Urmiana. During the last three decades, several considerable man-made changes including river damming and construction of a causeway across the lake affected the lake salinity. This article aims to propose a new approach of salinity modeling using a reduced-order model based on MIKE21 simulation model, in conjunction with principal component analysis (PCA) technique. At first, spatial variation of salinity in the lake was simulated by MIKE21 to prepare the input information for the PCA. Then, the dominant modes of salinity were determined by PCA technique while MIKE21 simulated results were compared with the output of developed reduced order model. Findings indicated that MIKE21's results closely matched the experimental data collected by field study. Also, the first 10 PCs among 974 modes computed by the reduced order model conserved approximately over 93% of the system variance. Therefore, the reduced order model was sufficient to capture the variation of salinity in the lake using a few first PCs. In other words, it was generally found that improvements in the simulated salinity in the lake provided by reduced order model were comparable to MIKE21 simulations.