Knowledge of the current condition of a waterway and watershed, as well as a clear understanding of the changes, if any, that result from human interaction with these environments—including effluent discharges from industry—is a basic requirement for developing effective environmental management strategies. Among the many lessons learned in the United States after more than 40 y of environmental regulation stemming from Earth Day and the founding of the US Environmental Protection Agency in 1970 is a proper monitoring strategy. A proper monitoring strategy for waterways is crucial to generating useful environmental and ecological data and achieving the environmental management goals set by particular industries, government agencies, and other stakeholders. Monitoring programs that have vague objectives, unspecific indicators and inadequate sampling designs have been shown consistently to provide little useful information upon which to regulate human impact on the environment. Incomplete knowledge of current conditions coupled with poor monitoring strategies invariably wastes limited stakeholder resources and leads to inadequate water quality management and ecological protection strategies. When examining the present day questions about the effects of effluents from pulp and paper mills on aquatic systems it is difficult to separate legacy issues from the challenges that this industry faces today. Two decades or more ago, the debate among scientists, industry environmental managers, and regulatory agencies in the United States focused primarily on waste waters containing residual fiber materials and oxygen-depleting organic substances released from mills directly to receiving streams and the nature and extent of the physical and chemical impairments on aquatic biota and the ecosystem. A decade or more ago, the scientific debate shifted; debate focused on the environmental significance of chlorinated organic substances in effluent, which resulted from the use of elemental chlorine in the production process at bleached kraft paper mills. Over the past 10 y production process changes at bleached kraft mills to alternate bleaching technologies has led to the near elimination of chlorinated organic substances in effluent. Although the reputation earned during these debates linger, modern pulp and paper mills in the United States, using primary and secondary effluent treatment technologies and chlorine-free processes, have significantly altered the properties of mill effluents, in most cases meeting or exceeding the goals expressed by scientists and regulators in the past for the elimination of constituents from effluents capable of harming the environment. The debate about paper mill effluent, however, has not ended. Today, new concerns have arisen concerning natural substances in trees (e.g., phytosterols) that may find their way into mill effluents discharged to waterways and adversely affect fish reproduction (Hewitt et al. 2008; Dube et al. 2008). Throughout this history of debate, the answers to questions regarding effluent effects on the aquatic environment and waterway ecosystems have been challenging. There has been an inconsistent use of monitoring tools and approaches to meet the information needs of various State and Federal regulators, local stakeholders and research groups. From time to time and in different regions of the United States, regulatory agencies and other stakeholders have opted for assessment approaches based on short-term or long-term assessment methods, shifting measurement endpoints, and/or changing management goals. In all of these instances, the approach has rarely included the consideration of ecosystem level or landscape level indicators of environmental quality or included consideration of the ecological services provided by the target waterway in any meaningful context. The use of inconsistent monitoring methodologies to assess effluent effects has resulted in considerable disparity in data availability and debate about the conclusions that have been drawn about the extent or type of impacts on the aquatic environment attributable to paper mill effluent. The debate has continued to this day—though the focus may change from fiber and oxygen-depleting substances to chlorinated substances to phytosterols. According to the Environment Canada publication EnviroZine (2004), scientists in Canada conclude with a high degree of certainty that paper mill effluents adversely affect fish populations. Yet, a series of long-term experimental streams studies of warm water (NCASI 1983) and cold water (Hall et al. 1991; Haley et al. 1995) stream communities found little indication of adverse effects on fish or aquatic food webs at effluent concentrations considerably above those found in North American receiving waters. Regardless of whether at the core of the debate among scientists, industry environmental managers, and regulatory agencies, the differences of opinion are based on scientific disagreement or poor communication, there is a great need to find common understanding of the impact of paper mill effluents on receiving waters. Facing this challenge, the National Council for Air and Stream Improvement (NCASI), an independent, non-profit research organization that focuses * To whom correspondence may be addressed: thall@ncasi.org