Plankton plays a fundamental role in marine ecosystems by regulating major elemental cycles and supporting functions and biomass of higher trophic levels. However, under ongoing environmental changes, marine ecosystems are experiencing impacts that can be difficult to detect using conventional bulk indicators such as biomass or primary production. To address this challenge, we applied a combined approach of Mass Balance Models and Ecological Network Analysis to detect changes in plankton trophic web structure and function. We analyzed a 19-year time series from the North Sea Ecosystem Cruise conducted by the Norwegian Institute of Marine Research, comprising 197 samples collected between 2006 and 2024. Our analysis identified a functional reorganization in 2019 detected synchronously by BEAST change point detection algorithm across multiple Ecological Networks Indicators. The shift was consistent across coastal and offshore water masses, while total biomass and primary production exhibited inconsistent patterns. Statistical analysis indicated that the largest differences in trophic organization occurred during the bloom period suggesting a possible phenological changes in the bloom composition. The observed increase in silicate concentrations after 2019 may reflect reduced uptake by diatoms, potentially liked to a shift toward smaller phytoplankton size classes. Overall, the post-2019 system showed an increase in flows organization complexity and in trophic efficiency, changes that were not captured by bulk indicators. These findings suggest that recent changes in the North Sea plankton community reflect a reorganization of trophic interactions and energy pathways rather than a simple change in overall biomass or productivity. This study highlights the importance of integrating long-term monitoring with network-based analysis to detect and understand changes in marine ecosystems.