Northern Australia has been the focus of recent marine biodiversity research to support natural resource management for both industry and conservation, including management of the Oceanic Shoals Australian Marine Park (AMP). Much of this research has targeted habitat-forming sessile invertebrates and charismatic megafauna, but smaller macrofauna and infauna may also be important because of their roles in ecosystem functions. In this study we characterised the biodiversity of polychaetes collected from four marine surveys to the Oceanic Shoals AMP between 2009 and 2012 from which sediment samples were elutriated (500 μm) to separate macrofauna. We used this species-level inventory to examine several questions related to marine management, namely: (1) do polychaete assemblages vary among surveys; (2) can environmental variables or geomorphology explain differences in community structure; and (3) how do ecological patterns change according to taxonomic resolution (species, family) and functional group (feeding, habitat, mobility)? A total of 2561 individual polychaetes were collected from 266 samples, representing 368 species and 43 families, including new species and genera, as well as new family records for Australia (Iospilidae, Lacydoniidae). Polychaete species assemblages and functional groups showed variation among the surveys, but this was not observed at the family level. Species and family assemblages were weakly related to environmental factors, but functional groups showed stronger relationships. Plains and banks each supported distinct polychaete assemblages, although the latter showed temporal variation. The results provide baseline biodiversity and ecological data about polychaetes on the northern Australian shelf, and these are discussed in relation to marine management strategies. Notably, intersurvey and environmental patterns differ from those of larger sessile fauna (sponges) collected on the same surveys, highlighting the need to consider small macrofauna in monitoring programs of marine protected areas.