Differentials between the invertebrate biodiversity of seagrass (S) and of adjacent bare sediment (B) were investigated at 8 localities spaced along the axial gradient of an estuarine system, that at Knysna in South Africa; various assemblage metrics being compared at paired S/B stations. Little or no S:B differentials were found near the mouth, but significant increase in those between both levels of overall assemblage abundance and of taxon richness did occur upstream (in abundance from <1 near the mouth to >2 towards the head, and in taxon richness from 1 to 2). The habitat supporting greater abundance therefore switched along the gradient. The differential between numbers of co-dominant species in the assemblages also increased upstream, whereas that between levels of taxonomic distinctness decreased. Functional diversity, evenness and patchiness differentials, however, showed no significant upstream change; neither did values of Bray-Curtis similarity between the two habitat types. Most affected were the epibenthic- and subsurface-feeding assemblage components. As predicted, macrobenthic assemblages of seagrass and bare sediment reacted differently to the gradient, and seagrass enhanced macrobenthic biodiversity much more upstream. However, location along the estuarine gradient appeared an equally important influence on assemblage composition to presence or absence of seagrass. The evident context-dependent nature of such differentials urges considerable caution in the extrapolation of ecological indicators derived from local areas to wider regions.