Production from geothermal reservoirs in volcanic-igneous hydrothermal systems may be disturbed owing to the formation of authigenic minerals that reduce primary porosity and infill fissure systems. Crystallization may be induced by natural processes or human activity related to the reservoir exploitation. In volcanic and volcaniclastic rocks, zeolites and related authigenic silicate minerals commonly develop. Two selected study sites—Pauzhetka geothermal field in Russia and Smrekovec volcanic complex in Slovenia are characterized by extensive development of progressive stage medium- and low-temperature propylitization and zeolitization with similar mineral assemblages that reduced original reservoir rock porosity and permeability. Retrograde and overprinting reactions of argillitization commonly enhance porosity and permeability of rocks, but some other reactions, like from prehnite to laumontite, from laumontite to heulandite, and from laumontite to analcime, encountered in the Smrekovec volcanic complex reduced it appreciably. Retrograde reactions recognized in the study sites were not induced by the temperature drop only, but were accompanied by the change in chemical composition of reacting fluids. Chemical composition of interstitial waters produced from exploitation wells in the Pauzhetka geothermal field indicate that propylitic and zeolite facies alteration is related to Na–Cl, slightly alkaline waters, while argillitization involved acidic thermal waters with more complex ion composition.