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Long‐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. Plain Language Summary: The terrestrial biosphere features the largest global sources and sinks of atmospheric carbon. Changes in growing season length, disturbance frequency, human management, increasing atmospheric carbon dioxide (CO2) concentrations, amount and timing of precipitation, and warmer air temperature all influence the carbon cycle. Observations from the global eddy covariance flux tower network have been key for diagnosing these changes. However, data from most sites are limited in length. Here, we explore how multi‐decadal carbon flux measurements from a cluster of flux towers in forests and wetlands in the upper Midwest USA respond to environmental change. Despite the proximity of the sites, year‐to‐year variation in carbon fluxes was rarely similar between sites. Surprisingly, warmer winters promoting earlier snowmelt led to later spring green‐up because soil temperature was colder. Impacts of higher CO2 and warmer temperature on annual carbon fluxes were limited but did influence factors linking carbon flux sensitivity to climate. Differences in flux magnitudes from a very tall tower flux to the network show that the whole does not seem to be simply a sum of its measured parts. More elaborate approaches may be needed to understand the processes that control carbon fluxes across large landscapes. Key Points: Multi‐decadal eddy covariance flux tower site cluster provides insight into variation of regional carbon cyclingVariation of carbon exchange in two forests, two wetlands, and a tall tower responded differently to weather, phenology, and disturbanceChallenges in upscaling fluxes indicate need for advances in aquatic observations, disturbance mapping, and flux footprint decomposition [ABSTRACT FROM AUTHOR]