Native habitat at the delta is a mix of riparian woodlands and wetlands. A few miles east, the hardwoods give way to the conifer forests of the Cascades. The original hardwood forests were made up of black cottonwood, Oregon ash, willows and dogwoods. The delta's wetlands were full of cattails, rush and sedges.

Plentiful fish, birds and animal species were noted by the Corps of Discovery on their stop at the delta. The large sand deposits at the delta provided spawning habitat for the huge numbers of smelt and salmon that returned annually to the Sandy River. But before long–about 60 years later–fish runs were already declining.

The delta is critical for migratory birds and for breeding by neo-tropical birds. Waterfowl also use the delta for nesting cover during winter.