The Katarraktes cave system is located in northern Greece and is a complex of a rockshelter and a cave formed on the south river bank of Krousovitis River canyon (Serres, Macedonia region). The archaeological site area is well known as one of the most important archaeological sites in SE Europe since it hosts numerous archaeological findings dating back to the Early Bronze Age. Detailed stratigraphic analysis of three archaeological sections was performed in order to define the depositional conditions of the cave entrance facies sediments. Mineral magnetic properties were performed to enhance the paleoenvironmental interpretations and to detect sediment origins. Magnetic susceptibility (klf) obtained in high and low frequency as well as remanence parameters, such as saturation isothermal remanent magnetization (SIRM) and S-ratio, were measured in samples collected2from the archaeological sections. Results indicate a significant variability in the magnetic signal stored in the sedimentary record of Kataraktes cave system distinguishing between natural and anthropogenic sequences. The combination of the stratigraphic and magnetic results along with the archaeological data reveals that flood events of Krousovitis River and sediment accumulation from slackwater in the rockshelter area occurred around 3000 yr BC and were possibly the key factor for the abandonment of the prehistoric settlement.