Like any other open space in an urbanizing area, San Elijo Lagoon Ecological Reserve faces many problems. These include:
Hydrological changes making it difficult to maintain connection to the sea.
Pollutants accumulated in lagoon sediments and biota.
Nutrient loading from wastewater, storm water and urban runoff. Stimulated algal growth may result in eutrophication of system.
Loss of biological diversity due to restriction of "biological corridors". As development isolates the open space, species may not be replaced by new individuals if the existing population is lost. (Biological islands)
Loss of biological diversity due to invasion and displacement of native species by exotic (non-native) species, including escape of landscape plant species and predation by feral cats and dogs.
Continuing disturbance from infrastructure maintenance, involving work on easements for utilities, flood control projects, road maintenance, storm drain clearance, etc.
Ongoing pressure from the public to provide more trails, more different types of usage and activities, increased facilities and support, with the result that more people use the area, impacting the resource.