Currently, chemicals and waste are recognized as key drivers of habitat degradation and biodiversity loss in aquatic ecosystems. To ensure vibrant habitats for aquatic species and maintain a sustainable aquatic food supply system, Japan promulgated its Environmental Quality Standards for the Conservation of Aquatic Life (EQS-CAL), based on its own aquatic life water quality criteria (ALWQC) derivation method and application mechanism. Here we overview Japan's EQS-CAL framework and highlight their best practices by examining the framework systems and related policies. Key experiences from Japan's EQS-CAL system include: (1) Classifying six types of aquatic organisms according to their adaptability to habitat status; (2) Using a risk-based chemical screening system for three groups of chemical pollutants; (3) Recommending a five-step method for determining ALWQC values based on the most sensitive life stage of the most sensitive species; (4) Applying site-specific implementation mechanisms through a series of Plan-Do-Check-Act loops. This paper offers scientific references for other jurisdictions, aiding in the development of more resilient ALWQC systems that can maintain healthy environments for aquatic life and potentially mitigate ongoing threats to human societies and global aquatic biodiversity.