Deep waters are commonly associated with being unexplored, yet there are equivalent knowledge gaps about benthic macroinvertebrates (< 0.5 mm in size) that inhabit shallow, coastal sediments of Australia. Here, we present biodiversity and ecological insights gathered from macroinvertebrate sampling conducted over two sampling times in both deep (> 10 m) and shallow (≤ 10 m) areas of Cockburn Sound and Owen Anchorage, Western Australia. An overwhelming >21,000 invertebrate specimens comprising 482 taxa in nine phyla were documented (N = 60 samples). Over 36% of these taxa were rare, being found in just one sample. The most abundant invertebrates were detritus-feeding marine gastropods, filter-feeding bivalves, carnivorous polychaetes, and nematodes. While communities in shallow waters were, on average, more diverse and numerous in Cockburn Sound, the opposite trend was observed in Owen Anchorage. Cluster analysis revealed 12 unique communities across both sampling times, with environmental variables such as grain size, temperature and dissolved oxygen being important in structuring these communities. This study reveals a hidden world of invertebrates inhabiting coastal sediments, emphasizing the need to further explore this often-overlooked biotic element. Such research is vital as invertebrate communities play pivotal functional roles such as nutrient cycling and food provisioning.