Using principal component analysis and cyst diversity and equity trends, we can recognize four distinct dinoflagellate cyst (dinocyst) assemblages from four Rupelian (Early Oligocene) cores in the Mainz Embayment of the northern Rhine Graben (SW Germany). These assemblages are the Spiniferites ramosus (PC1), Thalassiphora pelagica (PC2), Homotryblium tenuispinosum (PC3), and Vozzhennikovia spinula (PC4) assemblages. The four cores provide an onshore–offshore transect in the Mainz Embayment. The H. tenuispinosum assemblage shows high factor loadings in proximal to intermediate cores, which is interpreted to reflect temporary high-salinity conditions. Mean dinocyst diversity and equity increase with distance from the Mid-Rupelian shoreline, indicating increasingly stable paleoenvironmental conditions towards the center of the Mainz Embayment. Within individual cores, changes in dinocyst assemblages through time are related to paleoenvironmental and paleoclimatological changes. The three proximal to intermediate cores show dominance of the H. tenuispinosum assemblage repeatedly alternating with high factor loadings of the T. pelagica assemblage. In both cases, dinocyst diversity and equity tend to be reduced. Highest factor loadings of the S. ramosus assemblage occur in intervals where neither of the above assemblages is dominant and tend to coincide with dinocyst diversity and equity maxima. We interpret this distribution pattern to denote different paleoceanographic conditions, reflecting drier and more humid phases in the Early Oligocene of Central Europe. During relatively dry periods, increased salinity conditions prevailed in proximal to intermediate settings of the Mainz Embayment, as reflected by the dominance of the H. tenuispinosum assemblage. During more humid periods, increased runoff led to higher nutrient availability and the formation of a pycnocline separating slightly less saline surface waters from higher saline deeper waters, thus impeding vertical circulation. These environmental conditions are documented in high loadings of the T. pelagica assemblage which is indicative of increased eutrophication and/or oxygen-depleted bottom waters. Transitions between drier and more humid periods, i.e. episodes of normal marine conditions, are characterized by high loadings predominantly of the S. ramosus assemblage as well as increased dinocyst diversity and equity values. We propose that the alternations between drier and more humid phases may be related to variations in the ocean–atmosphere moisture flux from the North Atlantic into Central Europe bearing a high-latitude climate signal.