The hydrogeochemical conditions of the development of a carbonate swamp that had formed in a previous sandpit were studied. The object is located in the town of Jaworzno-Szczakowa in the Silesian Upland of southern Poland. It has been shown that the sandpit, which has not been reclaimed since its operation ceased, underwent spontaneous processes toward the development of calciphilic vegetation. The Biała Przemsza River plays a significant role in supplying the swamp with water. The water of this river is highly contaminated because it receives wastewaters from zinc-lead (Zn-Pb) ore mines. Water that has high concentrations of calcium and magnesium ions favours the occurrence of calciphilic species (e.g., Liparis loeselii NATURA 2000 species), which form wetlands of carbonate vegetation that are rare in both Poland and Europe. The population size of this species on the studied swamp is a few hundred specimens. In addition to Liparis loeselii, there are other species that are protected or rare and endangered species at the national level and on the “red list” of Poland’s plants, hence such swamps could represent an important refuge for biodiversity.