We reconstruct the aquatic ecosystem interactions since the last interglacialperiod in the oldest, most diverse, hydrologically connected European lakesystem, by using palaeolimnological diatom and selected geochemistry datafrom Lake Ohrid "DEEP site" core and equivalent data from Lake Prespa core,Co1215. Driven by climate forcing, the lakes experienced two adaptive cyclesduring the last 92 ka: "interglacial and interstadial" and"glacial" cycle. The short-term ecosystems reorganizations, e.g. regimeshifts within these cycles substantially differ between the lakes, as evidentfrom the inferred amplitudes of variation. The deeper Lake Ohrid shiftedbetween ultra oligo- and oligotrophic regimes in contrast to the muchshallower Lake Prespa, which shifted from a deeper, (oligo-) mesotrophic to ashallower, eutrophic lake and vice versa. Due to the high level of ecosystemstability (e.g. trophic state, lake level), Lake Ohrid appears relativelyresistant to external forcing, such as climate and environmental change.Recovering in a relatively short time from major climate change, Lake Prespa isa resilient ecosystem. At the DEEP site, the decoupling between the lakes'response to climate change is marked in the prolonged and gradual changesduring the MIS 5/4 and 2/1 transitions. These response differences and thelakes' different physical and chemical properties may limit the influence ofLake Prespa on Lake Ohrid. Regime shifts of Lake Ohrid due to potentialhydrological change in Lake Prespa are not evident in the data presentedhere. Moreover, a complete collapse of the ecosystems functionality and lossof their diatom communities did not happen in either lake for the periodpresented in the study.