Seagrass
Submerged aquatic vegetation is the term used to describe rooted, aquatic flowering plants which include true seagrasses and freshwater plants. These plants perform a number of important ecological functions in both estuarine and freshwater systems and generally their presence in a system is considered a good thing. The vegetation influences the quality of the water and sediments by taking up nutrients and reducing sediment re-suspension. They also provide a refuge for macroinvertebrates and fish, and food for fish and wading birds, such as the Black Swan.
Seagrasses are increasingly being used as a tool to describe estuary condition. The distribution and species present within an estuary are dependent on a range of conditions such as water movement, sediment condition, fresh water supply and connectivity to the ocean. These aspects vary from estuary to estuary, so we expect seagrass communities to differ between estuaries.
There are common factors that influence the distribution of aquatic plants. These include changes in light, nutrient availability, grazing pressure, flood events and direct physical disturbance by humans.
Loss of seagrass habitat is generally equated with ecosystem decline and is most frequently linked to eutrophication (nutrient and organic loading) from the catchment. Phytoplankton blooms and excessive growth of macroalgae are both symptoms of eutrophication. Both phytoplankton and macroalgae reduce light availability for seagrass growth which in extreme cases can lead to seagrass loss due to shading effects.
Cockburn Sound and the Albany Harbours are both examples of the replacement of seagrass by macroalgae as a result of excessive nutrient inputs. 
The Department of Water assesses the state of seagrass communities by measuring changes in the species composition, distribution and cover of the seagrass communities in the estuary. The department has also identified more complex physiological indicators such as productivity, reproductive success and tissue nutrient content to describe the resilience of seagrass. This information is important as it tells us if seagrass habitats are being lost and if this loss is permanent or recoverable.
Common species of seagrass in Western Australian estuaries include: Halophila ovalis, H. decipiens, Ruppia megacarpa and Zostera muelleri.
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