Multivariate latent structure methods were used to determine environmental factors that influenced the distribution of magnetic susceptibility, calcium carbonate, organic carbon, stable oxygen and carbon isotopes, ichnofossils, calcareous nannoplankton and benthic as well as planktonic foraminifera in the 102 m long section of late Early Badenian age (Middle Miocene, Upper Lagenidae Zone) cored at Baden-Sooss for scientific investigations. Five factors ‘temperature’, ‘eutrophication’, ‘water stratification’, ‘oxygen-rich particulate organic material’ and ‘surface productivity’ controlled the variables to different degrees. The tectonically unaffected deeper part of the section (38 m to 102 m) started with a short warm period possibly characterizing environmental conditions of the preceding Lower Lagenidae Zone. A long ‘warm’ period from 78 m to 92 m followed the first temperature decline between 92 m and 100 m. Increased terrestrial input caused by intensified weathering through seasonal changes characterized warm periods. The subsequent long ‘colder’ period between 49 m and 78 m is distinguished by increased oxygen depletion, mixed water masses and dysoxic bottom conditions preferring carbonate and organic carbon production as well as inbenthic foraminifera. The following ‘warm’ period with decreasing oxygen depletion is abruptly finished between 36 m and 38 m in the sedimentary record through tectonic deformation. In the following period, ‘colder’ water conditions dominated interrupted by short warmer intervals, finally tending to warmer water at the top of the cored interval (8 m to 16 m). Although intermediate temperatures prevailed in the youngest period, oxygen depletion remained relatively high after obtaining the maximum in the previous period. This increase in oxygen depletion toward the top of the section is reflected in rising δ¹³C isotope values together with decreasing temperatures, thus following — just after the Miocene ‘Monterey’ excursion — the slight global cooling trend between –14.7 and –13.9 Myr preceding the main Middle Miocene cooling period.