ABSTRACT: In the Franconian Alb, Germany, bedded carbonates and reef dolomites of the Upper Jurassic each represent a facies with syngenetic porosities; both facies are fissured and karstified, occur site by site, receive the same groundwater recharge and are subject to the same mode of land use. A comparative artificial and environmental tracer study evidenced that in reef dolomites matrix flow is in the range of metres per year, and in fissures of the bedded carbonates in the range of kilometres per day; additionally non-reactive tracer dilution is much stronger in reef dolomites (dispersivities >50 m) than in bedded carbonates (dispersivities <10 m). As a consequence, reef dolomites have higher storage capacities (porosities 6-10 vol.%) than the bedded carbonates (porosities <2.5 vol.%), which may lead to a long-term accumulation of contaminants in reef groundwater as far as it does not undergo microbial disintegration. Collecting micro-organisms by traditional water sampling and by incubation of sterilized rock coupons proved that microbial numbers and functional groups in the reef facies are more abundant under agro-than beneath forest lands, and very few microbial communities occur in old groundwater (>1,000 years). Obviously, the abundance of colonies and functional groups reflect the prevailing nutrient and energy supply of micro-organisms through the land use. Laboratory experiments with groundwater samples from the study area without and with incubated rock coupons resulted in low respectively high disintegration activities, which are attributed to the bio-films upon rocks. Since denitrification in water needs anaerobic conditions, while the redox potential of groundwater in the karst is in the range of +400 mV, it was supposed that under field conditions the bio-films provide a chemical environment, which may significantly differ from flowing water. This hypothesis has been proofed by field investigations through an enrichment of 34S and 180 in sulphates, both in the groundwater, and will be extended to 15N and 180 in nitrates.