<jats:p>The projected transition of the central Arctic Ocean (CAO) into a warmer, seasonally ice-free ocean requires more knowledge of this environment to predict changes in the structure and dynamics of its ecosystems. We aimed to compare the state and underlying processes of Nansen Basin and Amundsen Basin ecosystems observed in August–September 2021 and assess impacts of Atlantic Water inflow and fresher Transpolar Drift waters, respectively, on these ecosystems. The basins differed in features of sea ice, hydrography, and chemical and biological compositions. The near-slope open water in western Nansen Basin showed a clear fingerprint of warm, saline Atlantic Water, with larger vertical turbulent fluxes facilitating nutrient transport across the pycnocline and supporting larger standing stocks of bacteria, protists, and zooplankton. Pelagic primary production and microbial and faunal stocks decreased northward and into Amundsen Basin, likely due to lower nutrient concentrations, stronger stratification, and reduced light through the more continuous and thicker ice and snow cover in Amundsen Basin, possibly also impacted by seasonally declining light levels. Transpolar Drift signals included lower salinity, stronger stratification, and higher silicate concentrations in Amundsen Basin surface waters. Similarities to earlier observations included the increase in small-sized algae from Nansen Basin into Amundsen Basin and overall low faunal abundances in the CAO, suggesting that overarching patterns remained unchanged over past decades. Examples of species range extensions and notable taxon absences relative to earlier studies, however, could be due to borealization and changes in sea-ice conditions, respectively. Higher density ecosystem sampling and consistent time series are recommended to confirm such conclusions. The distinct basin differences call for a regional approach to future management of the CAO. We especially caution against using the area of strong Atlantic Water inflow in southern Nansen Basin as representative of the entire basin, let alone Amundsen Basin or the CAO.</jats:p>