Nitrogen isotopes have been widely used as indicators of depositional conditions in studies of ancient sediments. Bohai Bay Basin is a major continental hydrocarbon province in NE China, but nitrogen isotopic signatures of this lacustrine system (connected with the open ocean occasionally) have barely been investigated. We report a study of paleoenvironmental information recorded by N isotopic variations in the lower third member (Es3L) and upper fourth member (Es4U) of the Eocene Shahejie Formation in the Jiyang Sub-basin, southern Bohai Bay Basin. Paleosalinity (B/Ga, Sr/Ba, and S/TOC) and paleoredox (Corg/P, DOP, UEF, and Fe/Al) proxies and δ13Corg values were used to elucidate paleoenvironmental factors that affect N isotopic signals in the study core. Results indicate that δ15N values are positively correlated with paleosalinity proxies in the Luo-69 and Niu-1 drill-cores. Two possibilities may account for this: (1) a paleosalinity surge caused by marine transgression events led to stratification of the water column, creating an anoxic–suboxic deep-water layer and promoting denitrification in sediments; or (2) strong stratification of the water column impeded the upwelling process that brought nutrients to the upper water layer, weakening nitrogen fixation there. In marginal-marine intervals such as the Eocene Shahejie Formation, water-column salinity may play a critical role in regulating the δ15N signal. This study indicates that nitrogen isotopic compositions may aid paleoenvironmental and paleoclimatic interpretations of marginal-marine shale, particularly when applied together with multiple paleoenvironmental proxies to improve the understanding of ancient sedimentary conditions in marginal-environment.