One of the prominent features of northeast Mediterranean (NEM) Holocene climate are recurrent phases of cold and aridity; their impacts on the hydrological cycle remain at large unknown, as few existing paleohydrological records are either restricted to lake-level fluctuations or focus near the ‘8.2 kyr BP’ event. Here, we present the detrital record of Aliakmon River in Lake Loudias between 9500 and 3000 cal. BP. Magnetic susceptibility (MS) exhibits high correlation with mean grain size ( r = 0.7) of silt-sized fractions and is used as a proxy of the distal clastic input of Aliakmon River, whereas organic matter (OM), carbonate content (CaCO₃), water content (WC), and clay concentrations decipher sedimentological and biological processes in Lake Loudias. Periods of high hydrological activity were interrupted by short intervals of low river discharge at c. 9400, 8600, 8200, 7500, 7000, 6200, 5300, and 4500 cal. BP and during a multi-century event centered at 3500 cal. BP, in agreement with marine and terrestrial paleoclimatic reconstructions from NEM. With exception of the wet period between c. 8.6 and 7.9 cal. BP, periods of increased hydrological activity are synchronous to contraction of Pinus forests and increased sea surface temperatures and silt transport in the Aegean Sea. The long-term (~580 years) variability of MS is in-phase with southeast Europe pollen-inferred annual temperature variations and with North Atlantic Ice Rafted Debris (IRD) events.