This article is based on ongoing research at ITAM and selected results of the recent Interreg Danube Transnational project Living Danube Limes, which aimed to elaborate sustainable conservation standards for archaeological sites in river valleys. Heritage sites in river valleys are complex systems with context-specific characteristics and limited adaptability. The resilience of such complex heritage systems to the impact of natural and man-made disasters can be improved by means of three basic approaches: i) preventive protection, ii) adaptation and iii) resilience preparedness. Preventive protection is cost demanding, not always feasible, and can sometimes lead only to partial benefits. It can be designed and implemented at territorial, building (ruin) and material levels. Adaptation is also cost demanding and may negatively influence the cultural heritage context and values. Resilience preparedness combines all the above-mentioned approaches, involves the public to a greater extent, and has proven effective in complex situations, such as in the protection of cultural heritage systems. This resilience-based approach was accepted as a core strategy for the Living Danube Limes project. Regular inspection, regular maintenance and preventive conservation are important elements of this strategy. Tips and procedures for the implementation of these activities are presented. Increasing resilience further requires understanding the critical elements of a cultural heritage system—a fundamental task for developing a resilience and risk management approach tailor-made for the cultural heritage system in question. The paper presents examples of such critical elements.