Marine long-term primary production trends are widely interpreted by the one-dimensional vertical stratification paradigm, which simplifies ecosystem responses to climate warming as a trade-off between limitation by light or nutrients. This open-ocean paradigm fails to capture complex biogeochemical shifts within estuarine-shelf marginal seas shaped by intense land-ocean interactions. We integrated 20-year satellite records with 2693 high-performance liquid chromatography (HPLC)-derived pigment measurements from 73 field cruises to investigate decadal changes of net primary production (NPP), phytoplankton size classes, and bloom phenology on the East China Sea (ECS) shelf. Contrary to the decline of NPP in oligotrophic offshore waters, there was sustained growth of productivity over the ECS inner shelf driven by microphytoplankton dominance and clear seasonal decoupling between frequent winter bloom pulses and prolonged spring biomass accumulation. Cross-model comparisons revealed opposing trends of NPP likely reflecting different sensitivities of chlorophyll- and absorption-based models to long-term ecological change. There was a pronounced contrast of model performance between shelf and offshore environments. Our results help explain both the limitations of the classical stratification paradigm and the divergent satellite-derived productivity outputs observed in marginal seas. Because shifts of phytoplankton size classes and phenological reorganization are underappreciated regulators of carbon fixation on river-fed shelves, there is a need for refined coastal models and multi-index ecological frameworks to improve global biogeochemical projections.