Lakes are sentinels of change in the landscapes in which they are located. Changes in lake function are reflected in whole-system metabolism, which integrates ecosystem processes across spatial and temporal scales. Recent improvements in high-frequency open-water metabolism modeling techniques have enabled estimation of rates of gross primary production (GPP), respiration (R), and net ecosystem production (NEP) at high temporal resolution. However, few studies have examined metabolic rates over daily to multi-year temporal scales, especially in oligotrophic ecosystems. Here, we modified a metabolism modeling technique to reveal substantial intra-and interannual variability in metabolic rates in Lake Sunapee, a temperate, oligotrophic lake in New Hampshire, USA. Annual GPP and R increased each summer, paralleling increases in littoral, but not pelagic, total phosphorus concentrations. Storms temporarily decoupled GPP and R, resulting in greater decreases in GPP than R. Daily rates of GPP and R were positively correlated on warm days that had stable water columns, and metabolism model fits were best on warm, sunny days, indicating the importance of lake physics when evaluating metabolic rates. These metabolism data span a range of temporal scales and together suggest that Lake Sunapee may be moving toward mesotrophy. We suggest that functional, integrative metrics, such as metabolic rates, are useful indicators and sentinels of ecosystem change. We also highlight the challenges and opportunities of using high-frequency measurements to elucidate the drivers and consequences of intra-and inter-annual variability in metabolic rates, especially in oligotrophic lakes.