The Patagonian Shelf is recognized for its high potential for carbon uptake, largely driven by intense biological productivity. While net CO2 uptake persists for much of the year, the mechanisms shaping sea–air CO2 fluxes (FCO2) during the less productive season remain poorly understood. Here, we examined surface FCO2 during autumn 2022 in the northern Patagonian Shelf, a region influenced by the confluence of the Brazil and Malvinas Currents, where strong submesoscale activity generates patchy flux regimes. Even under low-productivity conditions, chlorophyll-a (Chl-a) was the strongest predictor of FCO2: high Chl-a areas acted as CO2 sinks, whereas low Chl-a regions were near equilibrium or acted as net sources. Bloom phenology further explained coherent patterns, with sinks associated with off-season bloom peaks and sources linked to late-stage declines. The strongest uptake occurred in a retention zone offshore the upwelling front, where cyclonic circulation of the Malvinas Current concentrated pigmented cells. By contrast, in adjacent upwelling areas with higher advective flow, the upwelling of aged, carbon-rich waters promoted outgassing that offset biological uptake, underscoring the dual role of upwelling in carbon cycling. Planktonic assemblages also influenced carbon cycling. Prochlorococcus dominated oligotrophic waters under Brazil Current influence, where low Chl-a, depleted microbial abundances, and reduced fluorescent dissolved organic matter (DOM) reflected limited sequestration capacity and persistent CO2 outgassing. Conversely, Synechococcus, picoeukaryotes, and heterotrophic bacteria co-occurred in CO2 sink regions, where DOM showed signatures of recent biological production. On the shelf, abundant bacteria and viruses were associated with humic-like refractory DOM, suggesting microbial reworking as a pathway for long-term carbon storage. Together, these findings demonstrate how the interplay of physical transport, bloom dynamics, and microbial transformations generates a heterogeneous pattern of CO2 sources and sinks in the Brazil/Malvinas confluence.

The Patagonian Shelf is recognized for its high potential for carbon uptake, largely driven by intense biological productivity. While net CO2 uptake persists for much of the year, the mechanisms shaping sea–air CO2 fluxes (FCO2) during the less productive season remain poorly understood. Here, we examined surface FCO2 during autumn 2022 in the northern Patagonian Shelf, a region influenced by the confluence of the Brazil and Malvinas Currents, where strong submesoscale activity generates patchy flux regimes. Even under low-productivity conditions, chlorophyll-a (Chl-a) was the strongest predictor of FCO2: high Chl-a areas acted as CO2 sinks, whereas low Chl-a regions were near equilibrium or acted as net sources. Bloom phenology further explained coherent patterns, with sinks associated with off-season bloom peaks and sources linked to late-stage declines. The strongest uptake occurred in a retention zone offshore the upwelling front, where cyclonic circulation of the Malvinas Current concentrated pigmented cells. By contrast, in adjacent upwelling areas with higher advective flow, the upwelling of aged, carbon-rich waters promoted outgassing that offset biological uptake, underscoring the dual role of upwelling in carbon cycling. Planktonic assemblages also influenced carbon cycling. Prochlorococcus dominated oligotrophic waters under Brazil Current influence, where low Chl-a, depleted microbial abundances, and reduced fluorescent dissolved organic matter (DOM) reflected limited sequestration capacity and persistent CO2 outgassing. Conversely, Synechococcus, picoeukaryotes, and heterotrophic bacteria co-occurred in CO2 sink regions, where DOM showed signatures of recent biological production. On the shelf, abundant bacteria and viruses were associated with humic-like refractory DOM, suggesting microbial reworking as a pathway for long-term carbon storage. Together, these findings demonstrate how the interplay of physical transport, bloom dynamics, and microbial transformations generates a heterogeneous pattern of CO2 sources and sinks in the Brazil/Malvinas confluence.