In the Polish sector of the Magura Nappe have long been known and exploited carbonate mineral waters, saturated with carbon dioxide, known as the “shchava (szczawa)”. These waters occur mainly in the Krynica Subunit of the Magura Nappe, between the Dunajec and Poprad rivers, close to the Pieniny Klippen Belt (PKB). The origin of these waters is still not clear, this applies to both “volcanic” and “metamorphic” hypotheses. Bearing in mind the case found in the Szczawa tectonic window and our geological and geochemical studies we suggest that the origin of the carbon dioxide may be linked with the thermal/pressure alteration of organic matter of the Oligocene deposits from the Grybów Unit. These deposits, exposed in several tectonic windows of the Magura Nappe, are characterized by the presence of highly matured organic matter – the origin of the hydrocarbon accumulations. This is supported by the present-day state of organic geochemistry studies of the Carpathian oil and gas bed rocks. In our opinion origin of the carbon-dioxide was related to the southern, deep buried periphery of the Carpathian Oil and Gas Province. The present day distribution of the carbonated mineral water springs has been related to the post-orogenic uplift and erosion of the Outer (flysch) Carpathians.