jats:pLow field magnetic susceptibility (MS) records of 13 reference boreholes representing the whole Quaternary fluvial succession of the Great Hungarian Plain were correlated to develop regional stratigraphy. Data from 12 of the boreholes were published between 2016 and 2020, the Tiszainoka borehole is newly reported in this paper. Eleven magnetic susceptibility cycles, capped by the most emergent master MS peaks (MP) and bordered by susceptibility termination surfaces, have been correlated. Supported by the already evaluated palaeomagnetic reversals and instability events, MPs have been correlated to the cold stages of the Marine Isotope Stage (MIS) records. MPs represent MIS 104, 100, 98, 82, 60, 52, 34(−36) and 26 of increased heavy oxygen isotope value, constituting the significant Early Pleistocene glaciations, and MIS 18, 16, 12, 8, 6 and 2 mostly representing the substantial Middle and Upper Pleistocene European glaciation events. The interpretation of early postglacial fluvial MS maxima, which emphasizes the escape of weathering‐sensitive magnetic minerals from the catchment area triggered by the thawing of mountain permafrost, is confirmed by the correlation of MPs to the changes of the global ice volume. As a result, fluvial MS records can be considered as a proxy for mountain permafrost development in the catchment areas. Regional correlations confirmed that the Körös and Jászság Basins and the Makó Trough are sites of almost continuous fluvial records of the past 2600 ka. Thus, the Pannonian Quaternary fluvial succession is sufficiently complete to provide a satisfactory record of mountain permafrost development of the Alp‐Carpathian region, the latter being a globally relevant European representative of mid‐latitude mountain regions. The similarity of the Pannonian fluvial MS succession as a permafrost proxy to the marine ice‐rafted detritus (IRD) and Chinese loess/palaeosol MS records promises the possibility of comparative investigations of globally relevant proxy records and mid‐latitude mountain permafrost development.</jats:p>