This chapter presents a comprehensive assessment of current challenges and strategies for water resources protection and management in the northern Qinling Mountains. This ecologically vital region, while rich in surface and groundwater resources, faces mounting pressure from climate change, population growth, urbanization, and intensive land use. The chapter outlines key issues in water quantity, including declining runoff, groundwater overexploitation, and reduced ecological baseflow, and water quality with rising concerns over industrial, domestic, and agricultural pollution, particularly nitrate contamination. The ecological environment is further threatened by soil erosion, land degradation, habitat fragmentation, and recurrent natural hazards such as landslides and floods. In response, the chapter reviews legal frameworks, ecological policies, major infrastructure projects (e.g., Han-to-Wei and Hongyan–Shitou River transfers), and ecological restoration programs. It highlights integrated management approaches to coordinate surface water and groundwater use, restore damaged ecosystems, and mitigate pollution. The chapter concludes with forward-looking recommendations for sustainable water governance, emphasizing legal enforcement, scientific research, public participation, and coordinated conservation to ensure the Qinling Mountains’ long-term ecological security and its role as China’s central water tower.