The Polish Lowlands, located southwest of the Teisseyre-Tornquist Zone, within Trans-European Suture Zone, were affected by bimodal, but dominantly rhyolitic, magmatism during the Late Paleozoic. Thanks to the inherited zircon they contain, these rhyolitic rocks provide a direct source of information about the pre-Permian rocks underlying the Polish Lowland. This paper presents zircon U-Pb geochronology and Hf and O isotopic results from five drill core samples representing four rhyolites and one granite. Based on the ratio of inherited vs. autocrystic zircon, the rhyolites can be divided into two groups: northern rhyolites, where autocrystic zircon is more abundant and southern rhyolites, where inherited zircon dominates. We suggest that the magma sources and the processes responsible for generating high silica magmas differ between the northern and southern rhyolites. Isotopically distinct sources were available during formation of northern rhyolites, as the Hf and O isotopes in magmatic zircon differ between the two analysed localities of northern rhyolites. A mixing between magmas formed from Baltica-derived mudstone-siltstone sediments and Avalonian basement or mantle can explain the diversity between the zircon compositions from the northern localities Daszewo and Wysoka Kamieńska. Conversely, the southern rhyolites from our two localities contain zircon with similar compositions, and these units can be further correlated with results from the North East German Basin, suggesting uniform source rocks over this larger region. Based on the ages of inherited zircon and the isotopic composition of magmatic ones, we suggest that the dominant source of the southern rhyolites is Variscan foreland sediments mixed with Baltica/Avalonia-derived sediments.