The EU Green Deal has direct and indirect impact on EU environmental law. We examine the future of EU regulatory activity on waters in this era from the viewpoint of industrial water pollution. We simultaneously explore the feasibility of Gunningham’s classic categorization of environmental law, regulation, and governance in the novel reality created by Green Deal and Nature Restoration Law (NRL). In the EU, the relations between the regulation (Water Framework Directive, WFD) and law (Industrial Emissions Directive) (IED) layers have been particularly tense. Although the Court of Justice of the European Union (CJEU) has attempted to clarify the situation, significant diversity remains at the Member States level, as our account from two Member States, Finland and Germany, illustrate. Though the EU has opted for and continues to embrace integrated and holistic water management integrated water resources management (IWRM), it would also be possible to adopt other regulatory strategies. An example of this, and of collaborative governance, is China, where the River Chief System (RCS) has moved on from IWRM. The EU’s chosen path seems, however, to lie elsewhere, as our function analysis of the proposed NRL shows. Through the NRL, the EU regulator declares to ‘fill the gaps’ of the WFD. This new reality of EU ‘aquatic biodiversity governance’ seems to create another layer in the traditional categorization of environmental law and governance, where all pre-existing EU environmental law is harnessed to combat (aquatic) biodiversity loss. Instead of managing waters, the NRL seeks to perfect the WFD but does not address its shortcomings, leaving room for concern.