Invertebrate faunas associated with vegetated and unvegetated habitats were sampled over a 15-month period in Western Port, Victoria, in order to identify consistent faunal differences between the two habitat types. Intertidal seagrass habitats in Western Port supported much higher numbers of macroinvertebrate species per 150 mm core (xBAR = 33) than intertidal unvegetated habitats (xBAR = 15 species), with a mean of 17 species per core found in the deeper unvegetated channel habitats. Species within channel habitats were more patchily distributed than elsewhere; consequently, the total number of species collected from channel habitats over all sampling occasions was high (265 species) and close to that collected from seagrass habitats (300 species), with a lower number (185 species) collected from intertidal unvegetated habitats. Estimated annual epifaunal production was much higher in intertidal seagrass habitats (17.2 g.m-2.yr-1) than in unvegetated habitats (3.3 g.m-2.yr-1). A substantial decline in seagrass cover in Western Port over the past twenty years is inferred from these data to have reduced epifaunal production by an estimated almost-equal-to 2500 tonnes ash-free dry weight (AFDW) per year within the bay. Annual infaunal production differed little between intertidal seagrass (62 g.m-2.yr-1) and unvegetated habitats (54 g.m-2.yr-1), so total infaunal production has probably changed little over that time. However, infaunal production was significantly correlated with the amount of organic material in the sediment, so long-term declines in infaunal production may have occurred as a consequence of declining production levels of seagrass detritus. Two corers with different diameter were used to obtain data on faunal size-distribution patterns within the 125 mum to 16 mm animal size range. Small diameter (50 mm) corers were significantly more effective at sampling benthos < 2 mm sieve size than large diameter (150 mm) corers. Faunal size-distribution patterns differed greatly between sampling locations, and meiofauna and small macrofauna were disproportionately abundant in the presence of seagrass. While faunal size-distribution plots were polymodal at most sites, production was rarely low at the macrofaunal/meiofaunal boundary, and size-related maxima and minima did not correspond with modes in sediment particle sizes, as was expected following Northern Hemisphere studies.