Is division of marine animals into macrofauna and meiofauna merely an arbitrary convenience, or, as has been claimed, does their size difference render them distinct and independent entities evolved under different ecological constraints? To investigate this, the ecological patterns of meiofaunal distribution, abundance and composition were investigated across the disparate regions of Knysna estuarine bay (South Africa). The locality was represented by ten specific seagrass and bare-sediment sites at which the equivalent macrofaunal characteristics had recently been established. Thus it was possible to compare meiofaunal and macrofaunal responses to the same suite of contrasting situations. Nematodes, copepods and ostracods, totalling 95.7% of numbers, dominated the epibenthic meiofauna which showed low (but not necessarily locally atypical) abundance: per core sample values of 19-886 (mean 211) 10 cm-2. Numbers were subequal or greater in seagrass beds than in bare sediment, and peaked in the clean delta sands of the mouth. Relative abundance of total macro- and meiofauna showed a comparable pattern along the system’s longitudinal axis, but each major component taxon, whether macrofaunal or meiofaunal, responded differently to the gradients concerned and no common within-group or contrasting between-group macrofaunal or meiofaunal responses were apparent. Indeed the strongest correlation was between distribution and abundance of the meiofaunal harpacticoids and macrofaunal gastropods. The macrofaunal ’opportunistic polychaete to amphipod’ and meiofaunal ’nematode to copepod’ indices of ecological quality yielded differing (but in both cases unrealistic) results. The Knysna macro- and meiofauna did not behave as distinct and discrete ecological entities, their individual component taxa displaying disparate patterns independent of their allocation into the two size classes.