Protected heritage area management is challenged by conflicting priorities perpetuated by the real and perceived dichotomy between cultural and natural resource management, their practitioners, their disciplines, and their values. Current guidelines promote integrating cultural and natural resource management to ensure holistic management of all values within a protected heritage area. This paper uses the management of the Cave and Basin National Historic Site to illustrate challenges in protecting both historic and natural resources. A qualitative inductive study included analysis of interview and focus group data for the site and similar protected heritage areas. The gap between integrative policies and the tendency for uni-disciplinary approaches to the practice of managing protected heritage areas is investigated. Five barriers to integration, such as lack of awareness, and five methods for progress, including facilitated inclusion, are examined. The author proposes collaborative, sustainable, values-based practices for the successful integration of cultural and natural resource management.