AbstractWhile beta diversity has been implicated as a key factor in controlling resilience of communities to stressors, lack of long‐term data sets has limited the study of temporal dynamics of beta diversity. With a time series at two sites in excess of 40 yr, we investigated turnover of both species and functional traits in a system stressed by eutrophication and overfishing and undergoing climate change and invasion. The two sites, although located near to each other, differ in water depth (20 cf. 35 m), but both sites have displayed increased abundances of an invasive polychaete since 1990. We tested two hypotheses related to the effect of an invasive species; that taxa richness and turnover would decrease, and trait richness would increase post invasion and that trait turnover would increase between arrival and establishment of the invasive. Generally, we observed different dynamics at the two sites and responses not consistent with our hypotheses. We detected an increase in taxa richness at both sites and an increase in taxa turnover and number of traits at one site only. Trait turnover was higher prior to the invasion, although again only at one site. Disjunctive responses between species and trait turnover occurred, with the invader contributing in a nonrandom fashion to trait turnover. The lack of strong, consistent responses to the arrival and establishment of the invasive, and the decrease in trait turnover, suggests that effects of invasives are not only system‐ and species‐dependent, but also depend on community dynamics of the invaded site, in particular the assembly processes, and historical context.