The Arctic has warmed significantly over the past decades. However, the evolution of Arctic climate during the Holocene remains to be clarified in more detail, and regional factors controlling aquatic ecosystem evolution need to be better defined to grasp the sensitivity of lakes to rapid environmental change. Nettilling Lake was studied for changes in sedimentary diatom assemblages over the last 5 000 years. Lake water pH was reconstructed by applying a diatom-based lake water pH inference model. We hypothesized that the changes in diatom assemblages were driven by variations in lake water transparency and attendant water turbidity associated with the input of fine suspended solids from glacial meltwaters. Reduced underwater light resulted in greater abundance of planktonic over benthic taxa from ca. 5 000 to 3 000 yrs. cal. BP, followed by less turbid conditions and proliferation of benthic taxa during regional cooling. The lake water was slightly alkaline throughout the Holocene, ranging between pH 7.1 and 7.7. Our results support the notion that hydrological processes, dependent on climate variations, have a first-order influence on the regulation of the lake water pH through glacial meltwater inputs, which will likely continue to control the lake's long-term chemical and biological evolution.