Anthropogenic increases in the salinity of surface waters are referred to as secondary salinization. In surface waters, salinity levels can vary significantly due to various natural and anthropogenic influences. This article presents multi-decadal observations of changes in surface water salinity in the highly industrialized region in southern Poland. The case study of the Przemsza River is an example of the significant impacts of industrial, mainly coal mining, activities that have changed the chemical and biological characteristics of water bodies. The presented research revealed that impacts on salinity and water body status due to mining discharges will be difficult or even impossible to restore, considering the process of transition of the coal sector. In the Przemsza river basin, almost 42% less mine water was discharged in 2023 than in 1991. Parallelly, the salinity of mine waters discharged from deeper levels of active coal mines has increased due to the geochemical gradient (the total load of chlorides and sulfates was 534.8 MgCl−+SO42− per day in 1991, while in 2023 the total salinity load was 480.1 MgCl−+SO42− per day). Moreover, of the 19 active mine water discharges in 1991, only 11 remain in 2023, while the observed salinity of surface water in the Przemsza watershed increased rapidly from an average of 2000 µS·cm−1 to 6700 µS·cm−1 due to the significant drought and adverse hydrological conditions, which represent low flows never observed before (three times lower flows in the mouth of the Przemsza River in the period 2021–2023 compared to the previous decades 1991–2020). Impacts on water bodies will continue to occur regardless of mining activities in the area—it should be noted that at the end of exploitation, mine water rebound and flooding do not automatically reduce long-lasting impacts on surface waters. Therefore, salinization is a growing threat that might be amplified by climate change. While industrial and urban impacts on surface water change its characteristics, the future challenge of proper water management with a holistic approach is necessary with proper monitoring data collection and river flow-dependent and surface water salinity-dependent discharge of wastewater in the river basin.