Arundo donax chokes riversides and stream channels, causing flood control problems. It also crowds out native plants, resulting in a loss of habitat for native species. In fact, this reduction in habitat is one of the factors contributing to the low populations of the endangered least Bell's vireo. In addition, arundo increases the risk of fire in riparian habitats which further reduces the numbers of native plant species. Finally, arundo requires more water than the native vegetation, stressing an area that already has little available water. Arundo is an extremely prolific weed. It reproduces vegetatively, through rhizomes which root and sprout readily. This type of reproduction allows arundo to reproduce very quickly, and thus build large stands in an area. Once established, the underground roots can reproduce new plants despite efforts at removal. In order to successfully kill arundo, the underground network of roots must be completely removed, or killed with pesticides.

Tamarisk, or saltcedar, is an invasive weed found within the Santa Ana River Watershed. Saltcedars have deep tap roots which allow them to access deep water tables. This ability to use deep water can cause small streams and springs to dry up. Saltcedar also out competes native species, promotes wildfires, increases soil salinity, and increases sedimentation and channel blockage. The loss of native riparian habitat is a major threat to the survival of animals in the infested areas. While saltcedar provides some amount of shelter to native animal species, it is little food value for the native wildlife.

Mechanical, chemical, and biological control have all been used in the management of saltcedar. For extensive areas of saltcedar, chemical control (herbicide) has been the most effective. Systemic herbicides (those that kill from the root up) are recommended: they can be applied as a foliar or aerial spray, or applied to cut saltcedar. Mechanical methods (cutting, bulldozing) can be effective, but can also cause problems with soil erosion in the removal area. Biological control, by introducing insects that eat the saltcedar, can gradually reduce the amount of saltcedar in the area, but approximately 15-25% of the original infestation can be expected to remain perpetually with biological control methods.  SAWA has performed some tamarisk removal within the Santa Ana Watershed, often in conjunction with arundo removal.