California wetlands, streams, and watersheds have been dramatically altered by human activities over the past 150 years. The primary threats to wetlands are discharges of dredge or fill material, excavation, and habitat degradation from external stressors such as point and non-point source (NPS) pollution. Protecting and managing wetlands and streams are complicated by the fact that no single agency has authority over aquatic resources and multiple programs within an agency may have authority or regulatory control over wetlands. A comprehensive wetlands and riparian monitoring program is needed to in order to improve program coordination to sustainably manage wetland resources and the stressors that affect them. The purpose of this paper is to describe the basic components of a comprehensive wetlands and riparian assessment program, based on USEPAs recommended framework and provide recommendations on incorporation of existing wetland assessment tools into agency programs. This paper will: (1) present an overview of the existing tools; (2) discuss how these tools can be used to inform decisions regarding wetland and riparian resources, and improve coordination and efficiency of various State and Federal wetland programs; and (3) identify key technical and administrative actions necessary to achieve these goals.