In this study, geochemical and petrographic characteristics of veins from the Permian Boda Claystone Formation (Mecsek Mts., Hungary) are presented. Understanding the connection between these properties is vital in the reconstruction of paleofluid history and tectonic evolution of this potential high-level radioactive waste disposal site. Each of the observed four vein generations consists of several mineral phases and has complex evolution, which can be attributed to multiple diagenetic and tectonic processes. Syntaxial and antitaxial veins have been observed suggesting oscillatory advective and diffusive material transport mechanisms; however, veins associated with mobile hydrofractures have also been detected. The parent fluids with a predominant temperature of 100–150 °C and variable salinity (3.5–13.7% wNaCleq) originated potentially by mixing of connate brine with freshwater released by smectite-to-illite transition and isotope exchange with sedimentary minerals, which may have caused the observed δ18O values (−1.12 to 4.67‰, V-SMOW). In contrast to the most vein-filling mineral phases, a breccia cement phase precipitated from a low-temperature (<50 °C) and salinity (0.0–0.4% wNaCleq) meteoric fluid. In the pores of this breccia veins, late-stage fluid migration is verified. Therefore, these veins are of paramount importance for studying the isolation properties of the rock body.