Among its various targets on restoring natural habitats and ecosystems in the EU, the recently adopted Nature Restoration Law (NRL) introduces ambitious targets for restoring surface water bodies (SWBs) as well. Simultaneously, the Italian CAP Strategic Plan for the implementation of the Common Agricultural Policy 2023–2027 has been designed to enhance sustainable agricultural practices, including water resource management. This paper provides a comparative analysis of the synergies, gaps, and challenges between these two regulatory frameworks, focusing on sustainable water use in Italian agriculture. A two-level comparative matrix methodology is employed to evaluate the alignment between the NRL’s objectives for freshwater ecosystems and the measures taken by the Italian CAP Strategic Plan on water resources. The results highlight key areas of convergence, existing shortcomings, and necessary steps for aligning Italian agricultural policies with the EU’s water restoration goals. The findings offer insights for policymakers, researchers, and stakeholders engaged in water governance, biodiversity conservation, and agricultural sustainability.