Victoria is located in temperate southern Australia. In this region, species of the genus Zostera, Heterozostera and Halophila are the most common as they dominate in estuaries and coastal lagoons. Posidonia and Amphibolis are also found, mainly near estuary entrances, or in sheltered bays. Ruppia meadows are common in areas of high freshwater input.

A feature of estuarine habitats in this region is heavy winter-spring rains with associated high turbidity, followed by high salinity and low rainfall in summer.

Seagrass distribution is influenced by biogeography/ geomorphology and wave energy. The distribution and occurrence of seagrasses depends on the estuary type, i.e., drowned river valley, barrier estuary or coastal lagoon. Seagrass species composition and distribution is associated mostly with sediment type and with differing exposure to wave energy from the open ocean. Seagrasses are generally more abundant several kilometers upstream from the estuary entrance due to lesser tidal and wave disturbance. Seagrasses in coastal lagoons may also be affected by the frequency with which the lagoon entrance is open to the ocean or closed by shifting sand banks, changing conditions from brackish to saline.

In less protected areas dominated by sandy sediments mixed seagrass communities consist of larger, slower growing species such as Posidonia australis with small, faster growing species such as Heterozostera tasmanica and Halophila ovalis occupying the gaps between meadows and areas close to freshwater inputs. At the mouth of some bays and in areas dominated by sandy siliceous sediments and exposed to ocean swells in Victoria, the slow growing seagrass Amphibolis antarctica forms patches of varying sizes rather than extensive monospecific meadows. In these areas, nutrient inputs are low and sediments are nutrient poor.

Deep, oceanic seagrass beds of Posidonia australis and Amphibolis antarctica are also present to depths of 22m in clear non-polluted water. Their distributions are influenced by depth bottom type, wave energy and geomorphology. Most seagrasses in southeastern Australia are restricted to depths <20 m by light availability.

Agricultural development and poor catchment practices in some regions have resulted in high sediment and nutrient loads reducing light availability and favoring species which can tolerate lower light levels. In other localities, reduced freshwater flows (due to industrial and agricultural extraction) have increased salinities.