About 5 miles northeast of the town of Campo in San Diego County, Clover Flat is a 2 mile long valley with surrounding hills of chaparral dominated by chamise. Coast live oak flourishes along tributaries and shaded slopes. Desert transition vegetation and big sagebrush are also abundant. Willow is scattered throughout local wetland areas and a prominent former drainage of the Miller Creek aquifer.  The historic Carrizo Gorge Railway loops through the property.

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Clover Flat provides critical habitat for the endangered Arroyo toad and Quino Checkerspot butterfly. Management focuses on restoration and expansion of habitat for these special species and all others across the preserve.