Exploring the interdependence between watermass conditions and climate change in marginal marine regions is essential for gaining insights into contemporary environmental challenges arising from global warming. Salinity, a key parameter of watermass conditions in coastal areas, plays a crucial role in influencing nutrient availability, stratification, and the spatial-temporal distribution of redox conditions. Here, we focus on the cyclostratigraphic analysis of gamma-ray (GR) data obtained from Eocene strata in the Luo-69 drillcore from the Bohai Bay Basin (NE China). This analysis establishes a high-resolution astronomical time scale (ATS) for the lower third member of the Shahejie Formation (Es3l), spanning 39.04 Ma to 41.46 million years ago (Ma). Various proxies for watermass conditions, such as salinity, sedimentary structures, mineral content, total organic carbon (TOC), organic carbon isotopes and nitrogen isotopes (δ13Corg and δ15N), exhibit a strong correlation with 405-kyr long orbital eccentricity climate forcing. Notably, spectral analysis of salinity data (represented by the Sr/Ba proxy) reveals a clear astronomical control, with 405-kyr eccentricity cycles that align closely with variations in the GR data. Peaks in paleosalinity, as indicated by Sr/Ba (as well as B/Ga and S/TOC), correspond with maxima in 405-kyr long orbital eccentricity cycles in the GR data. As such, we infer that astronomical forcing regulated long-term changes in watermass conditions, likely through mediation of the East Asia monsoon system. Specifically, during eccentricity maxima, the basin would have experienced a warm and humid climate with pronounced seasonality and a robust summer monsoon. During such periods, increased continental runoff would lead to a rise in lake-levels, facilitating better connections with the ocean, and hence increased salinity. By contrast, during eccentricity minima, cooler and more arid conditions with weaker seasonality would result in lower lake levels which together with a global eustatic lowstand would result in as weakened connection with the open ocean restricting the ingress of seawater into the basin lowering salinity. Our dataset spans the Middle Eocene Climatic Optimum (MECO, ∼40.60–40.10 Ma), identified by elevated GR values and a conspicuous negative excursion in oxygen isotopes. This interval is characterized by a significant decline in salinity, likely attributed to enhanced freshwater runoff driven by an extremely warm and humid climate. The paleosalinity fluctuation recorded by the proxies B/Ga, Sr/Ba, and S/TOC in Bohai Bay Basin demonstrate the sensitivity of marginal-marine environment to subtle changes in climate driven by astronomical forcing. Our results provide new insights into how elemental salinity proxies can be utilized in paleoenvironmental reconstruction studies.