Oyster Harbour - Understanding estuary health

The interactive diagram below shows a vertical slice through an estuary, it compares healthy versus unhealthy (or eutrophic) conditions. Underneath is a more comprehensive description of indicators of estuary health.

Move the cursor over the diagram to see details about each ecosystem element.


A healthy, biodiverse estuary depends on low nutrient inputs flowing in from the catchment.

Vegetation near streams, drains and rivers acts as a natural filter removing nitrogen and phosphorus from the water. Low nutrient concentrations entering the estuary limits the amount of algae growth that can occur.

With low algae growth and low amounts of organic matter in the waterway, water is clear, allowing seagrasses to adsorb the sunlight, providing oxygen and stabilising sediments. Seagrasses also provide important habitats to aquatic life and provide food for waterbirds.


A eutrophic system has large amounts of nutrients entering the waterway through fertiliser run-off, animal effluent run-off and the release of nutrients from sediment under certain conditions.

The large amounts of nutrients cause excessive growth of algae, which can be microscopic (phytoplankton) or up to several meters long and visible with the naked eye (macroalgae).

Eutrophic conditions become a threat to the health of the estuary and aquatic life when they persist for long periods of time.

Bacteria that breaks down algae consumes dissolved oxygen out of the water.  The lack of dissolved oxygen can leave aquatic life with insufficient oxygen to survive and can cause chemical changes resulting in the release of more nutrients from the sediment.

This can cause a cycle which is difficult to rectify; excess nutrients cause an algal bloom, algae breaks down consuming dissolved oxygen and lack of oxygen causes the release of excess nutrients.

Algae and organic matter also block sunlight, stopping it from reaching seagrass. Seagrass helps stabilise sediment and oxygenate the water, and the loss of seagrass can contribute the cycle of eutrophication.

Stratification in water is an important feature of most estuaries. It relates to vertical differences in salinity: freshwater from the rivers tends to sit at the surface because of its lower density, whilst the denser marine water entering from the ocean makes up the bottom layers. These layers require energy to mix – either from wind, currents or shear due to movement between the two layers.

The strength and persistence of stratification varies within an estuary, seasonally and even daily, depending on the river flow, tidal conditions and distance from the ocean entrance. Stratification greatly influences estuarine chemistry and biology, especially the oxygen status of bottom waters. Strong stratification causes a physical barrier preventing the diffusion of oxygen from the surface to the bottom waters.

In estuaries with significant algal productivity, the bottom layer also has a large amount of organic matter which is decomposed by oxygen-consuming bacteria. Oxygen can be depleted rapidly and when stratification persists, low oxygen (hypoxic) or no oxygen (anoxic) conditions emerge. These conditions are inhospitable to bottom-dwelling animals, and no oxygen in the bottom waters gives rise to rotten-egg-smelling hydrogen sulfide gas, which is also toxic. Sediment chemistry is altered by anoxia, releasing sediment-bound nutrients and adding to eutrophication problems.

Diagram of how stratification works