<p>Karst aquifers are widely distributed in the Urals region, but they remain underexplored, especially in terms of the collection and analysis of long-term hydrological and hydrochemical data series. This study presents a hydrochemical characterization of the Shulgan River karst basin (Southern Urals). The basin spans an area of 45.8&#xa0;km² and is a prime example of carbonate karst comprising multiple lithologies in the Southern Ural Mountains. Data collected from 2010 to 2025 were analyzed by calculating key hydrological and hydrochemical indicators, clustering, multivariate statistics, and end-member mixing analysis (EMMA). The main features of the basin are its extensive allogenic recharge zone and the dominance of concentrated input. Surface runoff from an extensive catchment is intercepted by major sinks and diverted into deep phreatic conduits, bypassing soil-epikarst storage. This aquifer shape explains its high regulating power and extreme flood dilution. Under base flow conditions, the major recharge components are supersaturated or in near-equilibrium with carbonates. The potential of carbonate dissolution occurs only under flood-dilution conditions. The anthropogenic impact on the aquifer is limited to local pollution with nitrogen compounds and HNO₃-induced corrosion. Observations of autogenous vadose waters (accessed in Shulgan-Tash cave) reveal the domination of quick flow through the tectonic fractures’ networks under impact of the “piston effect” after recharge acts. In addition to conventional controlling mechanisms such as infiltration rate and CO₂ accessibility, the hydrochemical composition of these waters has been influenced by biogeochemical processes related to the cave microbiomes’ contribution into the nitrogen cycle (local acidification and HNO₃-induced corrosion).</p>