- Anza-Borrego Foundation
 - Borrego Springs - Nonprofit organisation acquiring land for the Anza-Borrego Desert State Park through donation or by purchase from willing sellers. - Floresta
- Nonprofit organisation that educates, assists, and develops programmes to combat the problems in third world countries caused by deforestation.
- Friends of Salk Coastal Canyon
- La Jolla - Seeks to protect an endangered habitat and sensitive open space area along California's coastline from the impacts of a building complex and a car park plan proposed by the Salk Institute.
- Jarrett Meeker Foundation, The
- La Mesa - Funding educational programmes for disadvantaged children about the environment, conservation, and wildlife in partnership with the San Diego Zoo.
- Lake Hodges Scientific Research Center
- Escondido - Not-for-profit research organisation dedicated to learning more about the unexplained phenomena related to Lake Hodges, and in particular, the Lake Hodges monster.
- Napalm in Fallbrook@
- Fallbrook
- Resource Conservation District of Greater San Diego County
- Escondido - Provides technical, financial, and educational assistance to help both rural and urban communities conserve, protect, and restore natural resources.
- Sacred Earth Society
- Fighting for the planet, its decimated forests, its indigenous exploited people, and animals that are being tortured and exterminated.
- San Diego Oceans Foundation
- Devoted to the stewardship of the region's marine waters and living resources.
- Sea of Cortez International Preservation Foundation, The
- La Jolla - Seeks to motivate change in policies for the purpose of preserving the biological diversity and ecological balance in the Sea of Cortez.
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