Basin-scale stratigraphic correlation is the fundamental base for successful reservoir exploration, and especially when dealing with cross-border areas. Differences in lithostratigraphic and chronostratigraphic nomenclature between sub-basins and countries often result in problematic estimations of reservoir geometries and potential. This study combines available biostratigraphic, biofaunal and lithofacies data, together with sequence-stratigraphical correlations of the Lower Jurassic from the Central European Basin (CEB), to propose a genetic-based framework of transgressive and regressive depositional units. The determination of four major biofacies environments, composed of (I) polyhaline open-marine/offshore environments, (II) upper mesohaline marine–brackish environments, (III) lower mesohaline brackish environments and (IV) low oligohaline to freshwater continental environments comprising very rare marine phytoplankton and terrestrial spores and pollens, were translated into 12 biofacies reconstructions of ammonite (sub-) chronozone levels. Variations of biofacies reconstructions in time and space were supplemented by biostratigraphically constrained large-scale progradational and retrogradational sedimentary architecture. Retrogradation is accompanied by increasing polyhaline environments and pinpoint basinwide third-order flooding events, whereas progradation is accompanied by decreasing polyhaline environments pointing to third-order regressions. The outcomes of this study support exploration of Lower Jurassic deep geothermal reservoirs or CO2storage sites in the eastern CEB (especially Germany and Poland).