This discussion paper presents a framework for spatiotemporal differentiation in ecological protection goals to assess the risks of pesticides in surface waters. It also provides a proposal to harmonize the different scientific approaches for ecotoxicological effect assessment adopted in guidance documents that support different legislative directives in the European Union (Water Framework Directive and Uniform Principles). Decision schemes to derive maximum permissible concentrations in surface water are presented. These schemes are based on approaches recommended in regulatory guidance documents and are scientifically underpinned by critical review papers concerning the impact of pesticides on freshwater organisms and communities. Special attention is given to the approaches based on standard test species, species sensitivity distribution curves, and model ecosystem experiments. The decision schemes presented here may play a role in the “acceptability” debate and can be used as options in the process of communication between risk assessors and risk managers as well as between these risk experts and other stakeholders.