Plants and animals in the region have been dramatically impacted by habitat loss and degradation, species invasion, and overharvesting,. Species remaining in these systems are often of high conservation concern. Historically the Tijuana River Valley has been subject to disturbances from military activity, ranching and agriculture. Much of the disturbed land has been colonized by invasive exotic plant species. Additionally sediment-laden flow events from Goat Canyon have resulted in high levels of ecological disturbance, creating large alluvial deposits that have been colonized and dominated by non-native plant species. Non-native species of primary focus include: tamarisk (Tamarix ramosissima), arundo (Arundo donax), castor bean (Ricinus communis), perennial pepperweed (Lepidium latifolium), black mustard (Brassica nigra), Sahara mustard (Brassica tournefortii), and chrysanthemum (Glebionus coronarium). The habitats affected by this include salt marsh, freshwater riparian scrub and alluvial scrub, all habitats that are relatively rare throughout the region and support sensitive species. The Stewardship Program works to control exotic vegetation in these disturbed areas through chemical application, manual removal, and planting efforts. The Stewardship Program also promotes enhancement of native plant diversity through native plant propagation and planting efforts.
The coastal dune system within the Tijuana River Reserve supports populations of Western snowy plover (Charedrius alexandrinus) and California least tern (Sterna antillarum), two species of regional importance that have lost much of their nesting habitat to coastal development. The Stewardship Program works to protect these populations through habitat delineation with fencing and signage; control of invasive iceplant (Carpobrotus edulis), a species that can occupy quality nesting areas; involvement in community outreach efforts such as volunteer-based beach monitoring and education; and through contracting and working with specialists for predator control and population monitoring activities.