The depth and breadth of the channel along a river varies, creating different features such as pools, shallow, rocky or sandy sections, as well as backwaters – stagnant or slow-moving bodies of water that have been cut off from the main part of the river. These features provide different habitats that support a variety of plants and animals. 

Threats to in-stream habitat include: 

• sedimentation which fills in pools
• artificial barriers preventing aquatic life moving along the river
• pest plants or animals that out-compete native species.

As of 2009, fish passage has been provided at over 150 locations across Victoria by building fishways or removing obstructions. This has reopened close to 7,000km of rivers to migrating fish, exceeding the target set for 2011. 

In working toward the 2011 targets, Catchment Management Authorities and Melbourne Water have also re-established 500 km of in-stream habitat since 2002.

In many cases, this has been achieved by literally putting back what was taken away many years ago.

• Large wood (also referred to as snags) has been replaced, mimicking the habitat provided by trees that fall into the water.
• Meanders have been reinstated to create habitat niches.
• Indigenous aquatic plant and fish species have been reintroduced.

Unstable bed and banks impact on channel form, vegetation growth and habitat for bank-living species such as platypus. In-stream and bank erosion works have established, including 541 bed stabilisation structures stabilising 453 km of river bed. Stabilisation works reduce erosion which can lead to the scouring of the river bed, the slumping of banks or damage to infrastructure.