The functioning of ecosystems is decisively dependent on the composition and distribution of the functional traits of the constituent species. We used trait analysis to represent aspects of marine benthic functioning, using a 20-year time-series (1992–2011) on macrozoobenthos collected annually at four monitoring sites in the southern North Sea. Temporal patterns of trait composition and taxonomic composition were compared to test whether they exhibited similar or contrasting responses to environmental change. Temporal changes in trait composition were more similar among monitoring sites than the changes in the taxonomic composition suggesting that trait compositions converge towards a common structure sculpted by common environmental drivers. The relationship between species richness and functional diversity displayed a power-shaped curve with a shallow slope, implying considerable functional redundancy among species. The temporal trends in functional diversity were relatively stable as compared to taxonomic diversity, with only two irregularities coinciding with exceptionally cold winter events in the North Sea in 1995 and 2009. Following the temporary changes in ecological functioning, the functional diversity returned to previous levels within one year. The rapid functional recovery of the benthic infauna confirms the self-organizing ability of the ecosystem in response to stressors and may be attributed to the high functional redundancy in the temperate shelf sea system of the North Sea.