Ever since it was identified as a speleogenetic process in the Guadalupe Mountains of New Mexico, USA, hypogene speleogenesis has become the focus of numerous research projects aimed at discerning between classical epigene caves and sulfuric acid or thermal caves. The first distinguishing characteristics that were recognized for hypogene caves were passage and cave morphology. The following step was the identification of rare minerals, specific for processes associated to hypogene speleogenesis. One other important step was the recognition of the importance of stable isotopes - mainly of S - in tracing the source of S and the chemical processes affecting it. Many of the caves now labeled as hypogene are fossil caves, in which presently the hypogene activity has long died off. Studies comparing stable isotopes from coexisting cave minerals and the waters that generate the cave are rarer. This extensive study encompasses a description of cave and passage morphologies, cave mineral assemblages, as well as hydrogeochemistry of thermomineral waters in a peculiar region of Romania. Băile Herculane (Cerna River Valley, SW Romania) is a spa town known since Roman times for its numerous thermal springs that were considered to have healing powers. These springs, along with wells drilled in the past century, are still being used for curative purposes in several treatment centers in Băile Herculane. The present study is important not only for the scientific data it produced, but also for economic purposes, as mixing of the thermomineral waters with meteoric sources is a major concern, due to the dilution it causes. The data presented here is based on multiple investigation methods, each specific to the analyzed material: powder X-ray diffractions, scanning electron microscope, electron microprobe (for mineral samples), sedimentological investigations (for cave sediments), stable isotope mass spectrometry (for water and mineral samples), field measurements (for water samples). The results presented here help to clarify the source of dissolved S species in the thermomineral water, the source of the water itself, as well as establish a connection between caves along the Cerna Valley and the thermomineral aquifers.