To assess the role of macrofauna-mediated sediment changes on nematode community recovery, we examined the temporal development of macrobenthos, nematode communities and sediment properties following hypoxia in 16 m2 replicated plots over a 6 mo period. Hypoxia drastically changed nematode community composition (i.e. reduced diversity and abundances of all dominant nematodes, except Odontophora spp.), but complete mortality, as was the case for the macrobenthos, did not occur. Macrofauna diversity recovered slowly, but community composition approached that of control communities after several months. In contrast, nematode diversity recovered to control values within 1 mo but, subsequently, decreased again; hence, no clear convergence towards the control community composition was apparent. This diversity decline and lack of community recovery was mainly attributed to abundance overshoots of the epistrate feeding nematodes Chromadora spp., Daptonema spp. and Ptycholaimellus ponticus in the treatments, which dominated the treatment community after 2 mo. Nematode community reassembling was strongly related to the coupled macrobenthos-environmental temporal development. The dynamics of 2 sediment characteristics, which were both mediated by the colonizing macrobenthos, are presented as possible determinant factors for this relationship: (1) low nematode post-settlement resuspension resulting from stable sediments at early macrofauna recovery stages and (2) enhanced nematode reproduction and settlement success in a dense microphytobenthos mat in relation to the temporal variation in macrobenthos grazing pressure and bioturbation. In conclusion, the strong relationships between macrobenthos recovery, environmental development and nematode community development after hypoxia highlight the importance of macrobenthos–sediment interactions in the recovery and structuring of nematode communities.