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. The Peruvian upwelling system hosts a marine ecosystem with extremely high productivity. Observations show that the Peruvian upwelling system is the only eastern boundary upwelling system (EBUS) with an out-of-phase relationship between seasonal surface chlorophyll concentrations and upwelling intensity. This “seasonal paradox” triggers the following questions: (1) what are the unique characteristics of the Peruvian upwelling system, compared with other EBUSs, that lead to the out-of-phase relationship, and (2) how does the seasonal paradox influence ecosystem functioning? Using observational climatologies for four EBUSs, we diagnose that the Peruvian upwelling system is the only one to reveal that intense upwelling coincides with deep mixed layers. We then apply a coupled regional ocean circulation biogeochemical model (CROCO–BioEBUS) to assess how the interplay between mixed layers and upwelling regulates the seasonality of surface chlorophyll in the Peruvian upwelling system. Our model reproduces the “seasonal paradox” within 200 km off the Peruvian coast. We confirm previous findings regarding the main contribution of mixed layer depth to the seasonality of chlorophyll, relative to upwelling. Deep mixed layers in austral winter cause vertical dilution of phytoplankton and strong light limitation, impacting growth. The effect of advection, though second-order, is consistent with previous findings for the Peruvian system and other EBUSs, with enhanced offshore export opposing the coastal build-up of biomass. In addition, we find that the relatively colder temperatures of upwelled waters slightly dampen phytoplankton productivity and further slow the build-up of phytoplankton biomass. This impact from the combination of deep mixed layers and upwelling propagates through the ecosystem, from primary production to export and export efficiency. Our findings emphasize the crucial role of the interplay between mixed layer depth and upwelling and suggest that surface chlorophyll may increase, along with a weakened seasonal paradox, in response to shoaling mixed layers under climate change.

Mixed layer depth dominates over upwelling in regulating the seasonality of ecosystem functioning in the Peruvian upwelling system