AbstractLong‐running eddy covariance flux towers provide insights into how the terrestrial carbon cycle operates over multiple timescales. Here, we evaluated variation in net ecosystem exchange (NEE) of carbon dioxide (CO₂) across the Chequamegon Ecosystem‐Atmosphere Study AmeriFlux core site cluster in the upper Great Lakes region of the USA from 1997 to 2020. The tower network included two mature hardwood forests with differing management regimes (US‐WCr and US‐Syv), two fen wetlands with varying levels of canopy sheltering and vegetation (US‐Los and US‐ALQ), and a very tall (400 m) landscape‐level tower (US‐PFa). Together, they provided over 70 site‐years of observations. The 19‐tower Chequamegon Heterogenous Ecosystem Energy‐balance Study Enabled by a High‐density Extensive Array of Detectors 2019 campaign centered around US‐PFa provided additional information on the spatial variation of NEE. Decadal variability was present in all long‐term sites, but cross‐site coherence in interannual NEE in the earlier part of the record became weaker with time as non‐climatic factors such as local disturbances likely dominated flux time series. Average decadal NEE at the tall tower transitioned from carbon source to sink to near neutral over 24 years. Respiration had a greater effect than photosynthesis on driving variations in NEE at all sites. Declining snowfall offset potential increases in assimilation from warmer springs, as less‐insulated soils delayed start of spring green‐up. Higher CO₂ increased maximum net assimilation parameters but not total gross primary productivity. Stand‐scale sites were larger net sinks than the landscape tower. Clustered, long‐term carbon flux observations provide value for understanding the diverse links between carbon and climate and the challenges of upscaling these responses across space.