Few studies have compared hyperbenthic communities among estuaries, in either New Zealand or elsewhere. This study presents the results of a single late summer survey of the lower reaches of 26 estuarine systems along the Otago coastline from the Clutha River to Oamaru, comparing hyperbenthic communities among both permanently open and intermittently closed estuaries. Intermittently closed estuaries are periodically closed from the ocean because of the formation of a berm across the mouth. A total of 33 taxa were captured with mysids and amphipods, the most widespread hyperbenthic taxa, being common in both permanently open and intermittently closed Otago estuaries. The mysid, Tenagomysis novae-zealandiae, and amphipod, Paracalliope fluviatilis, were widespread, found in 74% and 68% of all estuaries sampled, respectively. In contrast, most other taxa were present in relatively few estuaries, with 17 species recorded from only 10% of estuaries. There was a significant difference in the community composition among permanently open and intermittently closed estuaries. The results highlight the potential sensitivity of New Zealand estuarine communities to management regimes that may alter their open/closed status.