Water quality was recorded quarterly along the length of the Swartvlei estuary (2002–2014), while seagrass biomass and macrobenthic abundance were measured annually in intertidal sandprawn beds (2009–2014). Despite relatively stable, marine-dominated conditions the abundance of the sandprawn Callichirus kraussi recorded in the lower and middle reaches decreased significantly (p < 0.025), accompanied by an increase in seagrass biomass and the abundance of burrowing bivalves and the surface-grazing gastropod Nassarius kraussianus. No significant changes were noted in the upper reaches, where, unlike the lower and middle reaches, the size distribution and juvenile recruitment of C. kraussi remained relatively constant. The temporal data from the lower reaches showed a high, negative correlation between C. kraussi numbers and (a) seagrass (Zostera (Zosterella) capensis) biomass (r = -0.85), and (b) burrowing bivalve numbers (r = -0.69). These relationships were apparent in comparative samples taken from prawn and seagrass beds, where C. kraussi numbers were significantly lower and burrowing bivalve numbers were higher in a seagrass area than in the adjoining high-density prawn bed. These changes accord with previously demonstrated negative correlations between vegetation of sandbanks and abundance of C. kraussi, and with the demonstrable negative effects of sandprawns on bivalves and N. kraussianus. However, our study is novel in that it indicated that changes in enviromental conditions may shift the balance among these species.