Mountain streams constitute challenging habitat for many fish species due to rapid and variable flow, cool temperature, and limited food resources. Groundwaters recharge by karst spring may however mitigate harsh habit conditions of mountain streams providing niches for different fish species. This study aims to assess the suitability of mountain streams, replenished by karst springs, for various fish species like alpine bullhead, European grayling, brown and brook trout. The study was conducted in the Chochołowski Stream in the Western Tatra Mountains, Poland. The assessment of abiotic habitat is based on different characteristics of hydrological and thermal regimes as well as water chemical composition investigated between 01.09.2012 and 31.09.2014. The findings reveal that: 1) downstream variability of habitat abiotic conditions (such as water temperature, flow, water chemical composition) may affect the distribution of fish species, 2) karst springs contribute up to 100% of the stream’s recharge during periods of winter low flow, 3) karstic groundwater reduces the variability and amplitudes of stream water temperature and weaken the periodicity in water temperature associated with daily course of air temperature and solar radiation, 4) groundwaters prevent stream freezing in winter and moderate summer temperatures, 5) increasing mineralisation of water below the spring recharge may positively affect fish distribution. The findings underscore the importance of karst springs in modifying the abiotic conditions of fish habitat in mountain streams.