Adaptive land protection and management strategies are fundamental to accomplishing the stated species and habitat conservation goals of federal Habitat Conservation Plan (HCP) and California Natural Community Conservation Plan (NCCP) efforts. In San Diego County, the current NCCP reserve system includes more than 200,000 acres of protected lands, which are monitored and managed by multiple jurisdictions. The Wildlife Agencies (FWS and DFW, collectively), environmental groups, and reserve managers would like an improved understanding of how various threats and stressors may be affecting reserve performance for the benefit of 103 plant and animal species. The intent of this applied research project was to complement the existing species and habitat monitoring efforts in San Diego County by developing a program to assess the possible effects of human recreation on wildlife populations. Specific objectives for first phase of this project were to: (1) Develop recommendations for research studying the effects of recreation on wildlife species; and (2) Test methods for monitoring recreation and complete a pilot field study. The second phase of this study was to implement a well designed study that integrates species monitoring with recreation monitoring to systematically assess recreation's direct and indirect effects on sensitive wildlife species, to improve the understanding of the trade-offs inherent in multiple-use management of reserves, and to ensure that NCCP reserves are providing the required levels of protection and achieving the goals of the NCCP program.