Planktonic systems form complex interaction networks that are pivotal to marine ecosystem health and stability. However, the long-term responses of these interactions to multiple stressors, especially in dynamic coastal and estuarine ecosystems, remain poorly understood. We applied an information-theoretic modeling approach to monthly abundance data of 74 plankton taxa (2000–2020) from Helgoland Roads (German Bight, North Sea) to reconstruct dynamic interaction networks. Our aim was to explore community- and system-level network properties and their relationships with potential environmental drivers. On the community-level, we found that interaction types encompassing predator–prey relationships among species strengthened under high light availability and nitrogen-to-phosphorus ratios of 20–25, whereas interaction types involving both predator–prey and competitive relationships among species (e.g., mixotrophs that can both prey on and compete with autotrophs) intensified under low light and nutrient availability. The latter interactions intensified particularly after 2006. Since then, links from grazers to primary producers have also strengthened, closely associated with a decline in ambient nitrogen-to-phosphorus ratios slightly below the Redfield ratio of 16:1. The system-level properties of connectedness and resilience provided an abstract view of network behavior, revealing that the system’s maturation process was non-linearly driven by salinity and nutrient availability. Consistent with complex-systems theory, the interplay between connectedness and resilience indicated that under low environmental variability, the system became highly sensitive to small nutrient changes, potentially triggering a reorganization of the interaction structure. These results highlight the system’s dynamic response to environmental changes and advance understanding of plankton network functionality in coastal ecosystems.