<p>Water ecological environmental protection is undergoing a significant paradigm shift, moving beyond traditional pollution control to a more integrated approach that emphasizes the health of aquatic ecosystems. This process of orderly adaptation in response to uncertain stressors, termed authigenesis, represents a key scientific issue in the field. In this paper, the underlying processes of authigenesis, i.e., self-adaptation, self-balance, and self-recovery, which sustain the resilience of aquatic ecosystems, are explored. This study introduces the innovative concept of “emissions-accommodation synergy” and aims to achieve authigenesis by constructing a dynamic equilibrium between pollutant inputs and the capacity of water bodies to accommodate the pollutants. For the first time, this paper proposes a practical framework for achieving emission-accommodation synergy, focusing on four essential aspects: understanding the mechanisms of emission-accommodation cooperation, developing a multidimensional monitoring and assessment system, advancing innovative technologies for ecosystem management, and establishing intelligent management and control pathways. The study systematically explores water ecology authigenesis from the perspective of synergistic emission-accommodation, providing scientific pathways for ecological water restoration and offering a comprehensive and scientifically grounded approach for sustainable protection and restoration.</p>