jats:titleAbstract</jats:title>jats:p jats:list jats:list-itemjats:pAn extensive area of seagrass covering the shore of part of the South African estuary ranked highest in overall national conservation and biodiversity importance (the Knysna estuarine bay) was killed by a series of seasonal green‐tidal blankets of jats:italicUlva</jats:italic> starting in the late austral summer of 2015, leaving bare muddy sediment. An earlier (2011) survey of then seagrass macrobenthic assemblages at 27 stations along over 1 km of that shore was exactly repeated in 2018 after this event.</jats:p></jats:list-item> jats:list-itemjats:pAfter loss of seagrass, intertidal macrofauna became significantly less speciose (1:0.61), spatially and systematically more uniform (1:1.30 and 1:1.63), but more (not the usual less) abundant (0.62:1). Assemblage composition also changed, with polychaete numbers (small nereidids, spionids, fabriciids and an endemic paraonid) increasing from <50% of total macrofaunal individuals to >90% (although cirratulids decreased), whereas small malacostracan crustaceans (except the amphipod jats:italicGrandidierella</jats:italic> sp.) and microgastropods diminished to insignificant levels—microgastropods for reasons possibly unconnected with the green tide.</jats:p></jats:list-item> jats:list-itemjats:pComparison with areas not vegetated in 2014, however, indicated that although macrofaunal abundance was greater in the 2018 jats:italicUlva</jats:italic>‐induced bare areas, levels of per unit area biodiversity (number of species, species and taxonomic diversity per station) were comparable. This suggests that the effect of local loss of seagrass cover is context dependent, particularly with regard to pre‐existing local seagrass versus adjacent bare‐sediment differentials, and does not necessarily lead to any “degraded” state.</jats:p></jats:list-item> jats:list-itemjats:pDecreased local importance of small malacostracans may severely impact the region's usage by the adult and juvenile fish for which it is an important nursery and feeding ground.</jats:p></jats:list-item> </jats:list></jats:p>