In an attempt to reconstruct the paleoenvironments of deposition for the Middle Jurassic Baghamshah formation, samples collected from six outcrop sections along the Shotori swell were subjected to detailed geochemical analyses. Bulk geochemical and biological marker data indicate a logical trend of the variation of organic input, salinity, and oxicity within Baghamshah paleoenvironments across the studied area. An increase in terrestrial character from southern end towards the central parts of the Shotori swell parallels with a uniform increase in the oxicity and a decrease in the salinity. The northernmost sections are characterized by less terrestrial impact, reduced oxicity, and elevated salinity compared to the central and southern sections. These variations are interpreted in the framework of past geometric configuration and a hypothetical paleogeomorphologic model is tentatively proposed for the Middle Jurassic of the area. According to these results, the depositional setting of the studied formation decreased in depth from Section-1 towards Section-4, suggesting that the proximity of the latter section to the Yazd Block may have had a strong control over the observed geochemical variations. The terrestrial organic input and the oxicity of the environment are conspicuously low for northern sections and their salinity shows a sharp increase compared to other sections. We hypothesize that a fault plan exists across the northern and southern Shotori Mountains that had played an active role in creating the current geochemical variations.