In industrialised areas, teleost fish are often exposed to anthropogenic changes of the water quality. These often have negative effects on species with a narrow ecological range. Species with a wider ecological range, such as the three-spined stickleback (Gasterosteus aculeatus Linneaus, 1758), might benefit if water quality alteration reduces interspecific competition and/or parasite infection pressure. In the present study, we investigated sticklebacks in an inland brook, in which the inlet of warm and salty coal mine drainage water increases water temperature and changes the brook from freshwater to brackish (approx. 20 mS cm−1) conditions. We collected sticklebacks up- and downstream of the saltwater inlet (henceforth called freshwater and saltwater sites or habitats) in monthly intervals from April to October 2010, and monitored their body condition parameters and parasite infections. In particular during spring, the water temperature was higher (3.7–4.5°C) in the saltwater habitat and juvenile sticklebacks occurred earlier and grew faster compared to juveniles in the freshwater habitat. In the saltwater habitat, fewer parasite species were detected compared to the freshwater situation (7 vs. 10). Moreover, parasite index, which peaked in young-of-the-year sticklebacks in September, was lower in sticklebacks from the saltwater site. The present study suggests that changes of freshwater conditions by the inlet of warm and salty coal mine drainage water match the adaptive range of three-spined sticklebacks, which grew faster and had lower parasite burden in the altered habitat.