The Upper Kimmeridgian Members “Calcaires blancs supérieurs” and the “Marnes à exogyres supérieures” of the southeastern Paris basin were investigated for their palynofacies and calcareous nannofossils. These members display alternating limestone-marl lithotypes and represent shallow marine palaeoenvironments. The lower carbonate member is interpreted as a proximal palaeoenvironment (palaeobathymetry = 5 to 10 m), where storm and swell deposits were prevalent and the salinity was occasionally weak. The relative richness of brown phytoclasts in this part is favoured by good preservation related to restricted conditions. These conditions would explain the dominance of the nannofossil Cyclagelosphaera margerelii in the nannofossil assemblages. The palynological data as those of the nannofossil assemblages show variations in the shift from carbonate member to marly member. The dominance of brown phytoclasts over black phytoclasts, the presence of amorphous organic matter (AOM), and the highest abundance and diversity observed within the nannofossil assemblages suggest that the maximum of distality occurred during this transition, at the basal part of the Marnes à Exogyres supérieures. The upper part of the section (marly member) characterized by storm deposits and storm-coquina beds is deeper (palaeobathymetry probably between 10 and 40 m depth) than the lower part. Oxidizing depositional conditions prevailed and explained the abundance of black particles found in this upper part, while proximate cysts and elevated non-placolith coccolith abundances indicate that relationships with the open sea were probably more significant compared to the lower part. Towards the top of the section, recurrences of restricted conditions are reflected by relatively elevated amounts of AOM and the abundance peak of the nannofossil Biscutum ellipticum. This study shows that micropalaeontological signals can be well recorded in vast lagunal domains. We speculate that salinity, nutrient supply, and oxygenation of the waters control microfossil associations. In shallow environments, these parameters are particularly fluctuating, especially when freshwater dilutes marine waters in surface, on the occasion of rainy periods or of intense arrival of continental waters.