Cenomanian-Turonian sediments of the Western Interior Seaway (WIS, North America) and Callovian shales of Western Europe were deposited in epeiric seas that connected the Boreal Sea to the Tethys. Samples from two cross-basinal transects of the WIS (southern Canada and southwestern USA) and from a latitudinal transect of the Callovian seaway (from Scotland to Northern France) were analyzed for their molecular fossils. Comparison of organic geochemical data (e.g. distribution of isorenieratane, an indicator of photic zone euxinia) with paleontological data (ichnofacies and benthic assemblages) suggests a dynamic water column structure with high frequency (annual to decadal) changes in benthic water oxygenation. During the transgressive and regressive phases, the southern WIS was frequently euxinic. At highstand, the southern WIS was more oxygenated with rare 'intermittent anoxic events'. In contrast, the northern WIS shows a continuous record of recurrent photic zone euxinia throughout the Greenhorn Cycle. A latitudinal variation is also observed for Callovian sediments of Western Europe. A 'Dynamic Fresher-Water Lid' (DFWL) model is proposed to explain the dynamism of the water column structure during accumulation of these black-shales. This model describes the recurrence of a fresher water lid extending from the north. At higher latitudes, these seaways received more fresh water input from the landmasses adjoining them, and possibly from the landmasses surrounding the Boreal Sea. We propose that anoxia in these epeiric seas is dominantly controlled by eustasy, land mass geometry, and connectivity to a large fresh-water supply. The causes of anoxic and euxinic conditions are generally twofold: water column stratification prevents oxygenation of deeper water masses, while heterotrophic reworking of upper water column primary produced organic matter increases oxygen demand at greater depths. In the DFWL model, the ingredients for density stratification (fresh water) and productivity (nutrients) are supplied simultaneously.