Abstract The North Sea has been undergoing long‐term transformations driven by shifts in human activities and climate change, which have jointly reshaped the composition of marine communities. Despite existing studies, the functional mechanisms driving community changes remain poorly understood. Here, we analyzed a 43‐year time series of meso‐ and macro‐zooplankton (> 500 μ m) monitored at Helgoland Roads to assess long‐term changes in functional biodiversity. We applied functional diversity indices and trait‐based uni‐ and multivariate analyses to (1) investigate the temporal variability in functional biodiversity components, (2) relate structural community changes to environmental drivers, and (3) interpret patterns in the context of community assembly mechanisms. Our results reveal asynchronous changes across biodiversity components, with pronounced structural shifts occurring in the early 2000s. These shifts were tightly linked to modifications in the food web: feeding traits together with predation‐risk traits contributed most to diversity changes, shaped by the abundance of diatoms and fish biomass. Environmental filtering processes could be identified as key mechanisms driving the reorganization of the community, leading to a significantly altered functional structure after 2005, with potential implications for food web dynamics and energy transfer to higher trophic levels. Our findings underscore the value of trait‐based approaches in gaining a comprehensive understanding of the mechanistic processes driving community change and support their integration into ecological models to improve projections of ecosystem responses under future conditions.