Assessments of spatial variability in lakes are often limited and extrapolations from a small number of sampling points increase uncertainty with respect to elemental budgets, and the underlying drivers of important processes such as primary production. We mapped surface water chlorophyll and CO2 on Lake Mendota, WI in Oct-Nov 2014 during fall turnover using a high-resolution sensor platform (> 35,000 spatially-distributed measurements). Surface water concentrations of chlorophyll and CO2 increased during lake turnover suggesting that the hypolimnion released stored nutrients and dissolved gas. Turnover increased lake-wide primary production and carbon dioxide efflux. Spatial patterns of chlorophyll and CO2 revealed strong contrasts across the lake’s surface. Littoral zones and river mouths had higher concentrations of chlorophyll and lower CO2 than pelagic zones. Spatial variability in these parameters was greatest in the nearshore areas, as complex sediment-surface water interactions lead to large variations in surface water conditions. While using single point observations in the middle of a lake may accurately represent metabolic and efflux rates across the pelagic zone, such datasets are not representative of processes in littoral and riverine transition zones.