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In Canada, Environmental Effects Monitoring (EEM) programs exist within two regulations: the Pulp and Paper Effluent Regulations and the new Metal Mining Effluent Regulations under the Canadian Fisheries Act. EEM provides a biological, effects-based feedback loop to assess the effectiveness of technology-based regulations in protecting receiving environments. The promulgation of the Pulp and Paper Effluent Regulations, in 1992, represented a significant step forward in the Canadian regulatory approach by incorporating directly into a regulation a requirement to assess the effects of effluent discharges on receiving environments using proven scientific monitoring methodologies. Similarly, an assessment of the aquatic impacts of mines resulted in recommendations to amend the Metal Mining Effluent Regulations, recently promulgated in 2002, and includes an EEM program as a science-based feedback loop. As such, these regulations recognize the possibility that national, technology-based standards may not necessarily protect all receiving environments because of the diversity and variability of both discharges and receiving sites across the country. Since that time, EEM has improved its flexibility by considering both advances in science and the uniqueness of monitoring sites across Canada to allow the most appropriate and cost-effective monitoring approaches at each site while maintaining national consistency. This paper discusses the use of monitoring under two Canadian regulations to assess effects on aquatic ecosystems. As well, the National EEM approach to maintaining up-to-date scientific practices in a national regulatory program is discussed using examples.