LakeAnalyzer is a computer program used to calculate indices of mixing and stratification, which are critical to understanding biogeochemical cycles of lakes and reservoirs. Lake physical stability indices, surface mixing depth and thermocline depth are calculated according to established literature definitions and returned to the user in a time-series format. LakeAnalyzer was developed to analyse high-frequency data collected from instrumented lake buoys (Figure 1). It provides a way to compare mixing and stratification indices in lakes across gradients of climate, hydrophysiography, and time, and provides a basis for understanding of the resulting biogeochemical transformations at different spatial and temporal scales.