In recent years, dredged material has become regarded as a potential resource and used to create and/or improve intertidal habitats (i.e., beneficial use). This paper presents the results of a sampling programme to investigate the long-term (42 months post-recharge) macro- and meiofaunal recolonisation processes of a beneficial use scheme in south-east England. While univariate indices of community structure indicated that the scheme’s meiofaunal community was never significantly different from that of a nearby reference area, such attributes for macrofauna were continually significantly below those of the reference area, although this was not the case for all reference stations. Multivariate analyses revealed that macro- and meiofaunal community structures were always significantly different from those of the reference communities. We discuss the factors responsible for these observations and propose that assessing recovery of a beneficial use scheme should be undertaken using pre-defined criteria in addition to comparisons with a reference site.