An integrated faunal and geochemical dataset has been generated by the study of a late Miocene (early Tortonian) sedimentary section outcropping at Manassi, Levkas Island (eastern Mediterranean). Quantitative analysis of benthic foraminifers from the 25-m-thick section indicates changes of bottom palaeoecological conditions in this part of the eastern Mediterranean, during the analyzed time interval. Benthic foraminifer assemblages are typical of a bathyal environment and testify to relatively oxygenated conditions with low to moderate food supply alternating with periods with an increase in organic matter content. The long-term palaeoceanographic analyses indicate an anti-estuarine circulation model based on the benthic foraminifer and stable isotope results, which evolved in a strong estuarine circulation. The positive relationship existing between the plankton d 18 O and d 13 C, in most of the record, agrees well with the hypothesis of a variable contribution of runoff. In three stratigraphic levels, samples record heavy bottom water d 18 O and d 13 C values and light surface d 18 O values, representing a wet, warm, estuarine climate with a stratified water column. In two stratigraphic levels, samples have depleted d 13 C and d 18 O values for both surface and bottom waters. These two samples represent wet, warm climates with some ocean mixing and stratification. The stable isotope signal of foraminifer tests from the Manassi section was influenced by the global temperature changes, but the local factors also played an important role. The palaeoenvironments derived from stable isotope analysis in this study are interpreted as responses to the local tectonic instability together with monsoon intensities that enhanced continental runoff, characteristic for the time interval studied in the study area. Due to the limited data available from this study, no correlations with the precessional, obliquity, or eccentricity cycles can be made.