Losses in lake area have been observed for several Arctic and Subarctic regions in recent decades, with unknown consequences for lake ecosystems. These reductions are primarily attributed to two climate-sensitive mechanisms, both of which may also cause changes in water chemistry: (i) increased imbalance of evaporation relative to inflow, whereby increased evaporation and decreased inflow act to concentrate solutes into smaller volumes; and (ii) accelerated permafrost degradation, which enhances sublacustrine drainage while simultaneously leaching previously frozen solutes into lakes. We documented changes in nutrients [total nitrogen (TN), total phosphorus (TP)] and ions (calcium, chloride, magnesium, sodium) over a 25 year interval in shrinking, stable, and expanding Subarctic lakes of the Yukon Flats, Alaska. Concentrations of all six solutes increased in shrinking lakes from 1985–1989 to 2010–2012, while simultaneously undergoing little change in stable or expanding lakes. This created a present-day pattern, much weaker or absent in the 1980s, in which shrinking lakes had higher solute concentrations than their stable or expanding counterparts. An imbalanced evaporation-to-inflow ratio (E/I) was the most likely mechanism behind such changes; all four ions, which behave semiconservatively and are prone to evapoconcentration, increased in shrinking lakes and, along with TN and TP, were positively related to isotopically derived E/I estimates. Moreover, the most conservative ion, chloride, increased >500% in shrinking lakes. Conversely, only TP concentration was related to probability of permafrost presence, being highest at intermediate probabilities. Overall, the substantial increases of nutrients (TN >200%, TP >100%) and ions (>100%) may shift shrinking lakes towards overly eutrophic or saline states, with potentially severe consequences for ecosystems of northern lakes.