Water conductivity in 23 lakes of the Suwałki Landscape Park (SLP) was tested in the years 2012–2014. Conductivity profiles were made at the deepest place every two months between spring and autumn water mixing. The collected measurement data, supplemented with historical data, were used to identify factors that shape the spatial variability of water conductivity and to reconstruct its multiannual changes. The range of variability of the mean conductivity of surface water of the SLP lakes ranged from 178 to 522 µS cm−1. The strong negative relationship between conductivity and lake elevation (R = 0.816, p < 0.000) suggests that in the territorially compact complex of the SLP lakes, conductivity is a consequence of the location of the lake in the catchment, which, in turn, affects the structure of its water supply. However, the physical and environmental parameters of the catchment and morphometric parameters of lake basins are of secondary importance. In dimictic lakes and in those showing signs of “spring meromixis”, the magnitude of conductivity differences in the water column is determined by the lakes’ susceptibility to wind mixing expressed by the exposure index value. The developed climate models have also shown that conductivity, an indicator of water quality, is very sensitive to climate change. The analysis of the reconstructed chronological conductivity sequences shows that the deterioration of the quality of the waters of the SLP lakes first occurred at the beginning of the 21st century and a clear increasing trend has been maintained over the last decade.