Environment Canada has revised its guidance manual for ecological risk assessments of priority substances under the Canadian Environmental Protection Act. This paper briefly summarizes the guidance provided on: problem formulation; data collection and generation; analysis of entry, exposure and effects; and risk characterization. The purpose of this paper is to discuss some of the difficult issues common to all programs conducting ecological risk assessments of substances, and to describe the approaches we have taken. Example issues include: (1) how should low toxic effects be determined, (2) how should risks be quantified, and (3) how can the ecological consequences of exposures to substances be determined? Finally, comments are provided on the process followed during the preparation of the revised manual. These comments are provided because we believe that the open and transparent process followed was beneficial to the identification and resolution of these and other difficult issues.