To what extent is the relative biodiversity of some flagship conservation sites a result of differential attention? Knysna estuarine bay is the topmost ranked South African estuary for conservation importance and biodiversity. It is also one of the most intensively studied, and hence differential sampling effort could partly be responsible for its apparent relative richness. To assess the extent to which this might be true, identical sampling area, effort and methodology were employed to compare the benthic macrofauna of one specific major Knysna habitat (Zostera capensis seagrass beds) with equivalent ones in two nearby lesser-studied estuaries, the Keurbooms/Bitou and Swartvlei. Investigation showed all three localities to share a common species pool, but different elements of it dominated the shared habitat type in each. The seagrass and adjacent sandflat macrobenthos proved just as biodiverse in unprotected Keurbooms/Bitou as in the Protected Area of Knysna, but that in Swartvlei (also a Protected Area) was impoverished in comparison, presumably consequent on mouth closure and the prevailing lower salinity. Despite marked geomorphological and hydrological differences, all three estuaries share a suite of unusual faunal elements and such particularly close faunal similarity suggests the importance of historical biogeographic processes. The analysis emphasises the need for caution when assessing the relative conservation importance or other merits of different individual systems in a data-limited environment.