Governmental water quality agencies are faced with identifying water quality goals to protect aquatic biota, applying the best available science in development of water quality standards and associated management principles, implementing water quality laws so that there is consistency with goals, developing guidance documents for applying science to law, monitoring, and enforcement. Deviations in this path from goals to standards to enforcement, however, are common across countries as well as among States within the United States and can result in failure to protect the aquatic biota.The Clean Water Act (CWA) is the key US law for water quality protection. Its goal is to ‘restore and maintain the chemical, physical, and biological integrity of the Nation's waters’ and to fully protect the most sensitive beneficial uses. The US Environmental Protection Agency (EPA) Gold Book guidance for development of protective water temperature standards, dating from 1973, still recommends the use of MWAT (Maximum Weekly Average Temperature) as an index for assigning protective chronic temperature standards to coldwater fisheries. MWAT, applied according to EPA guidance, is typically used in conjunction with an acute upper limit. Unfortunately, MWAT is a criterion that is not protective, as can be shown by reference to several case studies on salmonids. Use of MWAT at a basin scale can result in considerable reduction in available salmonid rearing area and can, in many cases, be little better than recommending the upper incipient lethal temperature as a standard. Although MWAT is not used by many US States in standards, it is problematic in that it is cited as the official EPA model for a protective standard. The conceptual use of MWAT highlights some critical problems in application of the Clean Water Act and its associated federal regulations for protection of coldwater fishes, such as the concepts of full protection, protection of the most sensitive species, restoration of water quality, and support of species' viability at a basin scale.Full implementation of the CWA in support of salmonids' thermal requirements has been patchy, with some States taking criteria development, monitoring, listing, and TMDL (Total Maximum Daily Load) development seriously and others virtually ignoring the problem. In addition, Section 316 of the CWA conflicts with the basic goals of the CWA by giving deference to the thermoelectric power industry to discharge heated effluent under a process where variances granted supersede water quality-based limits. This is exacerbated by EPA 316 guidance permitting evaluation of biological trends amidst shifting or uncertain baselines in a limited set of RIS (Representative Important Species), rather than application of best available science to protect both the most sensitive species and the entire aquatic community that is reflective of high quality habitat conditions. Designing water temperature standards to be fully protective and supportive of species viability (abundance, productivity, spatial structure, and diversity) benefits from application of concepts of optimum growth and survival temperatures distributed at a basin scale with reference to the natural thermal potential along a river continuum. Some notable successes in standards development found in the US Pacific Northwest are offered as future national models.