The Albanian–Thessalian Basin, which is located in the vicinity of Mount Morava, includes Eocene to Middle Miocene sediments with a poorly-known, calcareous nannofossil content. This study is focused on the investigation of calcareous nannofossil assemblages from the Lower Miocene sediments outcropping in the area, resulting in the correlation to the global nannofossils zones/subzones NN2–NN3/CN1c–CN2, as well as to the zonation from the Mediterranean area, where the MNN2b and MNN3a biozones have been identified. An early-middle Burdigalian age for the studied outcrops is supported by primary and secondary index species (Helicosphaera ampliaperta, Helicosphaera mediterranea, Sphenolithus belemnos, Sphenolithus disbelemnos, Sphenolithus pseudoheteromorphus). Quantitative analyses were performed on calcareous nannofossils and statistics were applied to all of the counted samples. Based on the statistical analysis, short-time fluctuations in palaeoenvironmental parameters, such as temperature, salinity and eutrophic regime, are documented through the changes in the calcareous nannofossil assemblages and their abundance patterns. The depositional palaeoenvironment indicates changes in basin water depth, with influence of cold upwelling currents, terrigenous nutrient influx, and increased palaeoenvironmental perturbations over short time intervals.