What is the scientific method by which we can derive standards or guidelines for water variables such as salinity, nitrate, phosphorous, etc., to assess the environmental condition of a particular river?
Water quality standards for specific sites such as a river are usually derived using a combination of literature information and on-site data. The critical step is to evaluate the river itself, not only to describe it's general character, but also to identify key species, processes or habitats that are in need of protection. The river may support a rare or important fish, or even a rich fish assemblage; there could be a problem with nutrient enrichment, or toxic substances, or a pH imbalance. A defensible water quality standard demands good data on the geography, chemisty and (especially) the biota of the river.
The next step is to use the literature to establish thresholds of effect for the variable in question. If we were considering pH, for example, a thorough literature review on the effects of pH on aquatic life, both direct and indirect, is necessary to support a guideline. Fortunately, this work has already been done in many other jurisdictions so there is no reason not to borrow or build on their foundational works.
The key step is then to modify the global standard according to the particular conditions in the river in question. For example, if we know that a fish assemblage or a fish species is highly demanding of oxygen, we may set a dissolved oxygen guideline that is higher than the general recommendation. Similarly, a specific guideline to avoid toxicity from a heavy metal may be erected if there is a problem with that metal in the river and a threat to a sensitive species. In this way, our accumulate knowledge of the variables, as described in the literature, is combined with quantitative data on the river itself, to create a guideline that is reasonable and scientifically defensible.
As suggested already, there are a variety of indicators or tools that can help assess water quality. Some are direct testing and compare with various standards already set for or specific to drinking, irrigation, industry, etc. Fish, macrinvertebrates, aquatic plants, algae are examples of potential biological indicators that aquatic biologists may use to help define or evaluate water quality. Some have developed protocols for biological testing and may be referred to as Index of Biological Integrity (IBI). Hydrologists and watershed managers evaluate the contributing lands called among other things, watershed assessments, used to evaluate land uses, pollution sources, available literature or data, etc. Sometimes public agencies or universities collect and maintain these records, and for public health or other reasons may have already done some classification. To some degree, people who use the water for fishing, drinking, irrigation, etc. probably have opinions (right or wrong) based on the waters clarity, smell, past or present observances or testing data taken under a variety of conditions, edibility of fish or other organisms, irrigation of crops, and utility for other uses. When the question leads to scientific defensible needs, a variety of professionals may be involved, or utilize toxicology and other assessments that can be applied, and have received technical review. As suggested, use and reliance on already set standards and Management practices as BMPs to address various activities to control point or non-point pollution. This activity is often addressed by environmental agencies with interaction with qualified professionals, as well as others such as landowners, industry, farming, forestry, urban, etc. A final standard or guideline product may never emerge, as changes in information as well as land uses, practices, water quality, etc. necessitate periodic review and adjustment. To some degree, and depending on the local circumstances, it is important to have review and support from country leadership and/or designated agencies, rules, regulations, etc. For example, if river irrigation of croplands is a common use for food production, one can imagine how well restrictions or treatments might be received by those landowners. And consider liability insurance such as engineers obtain to protect yourself and perhaps university if lawsuits might be used by those who don’t want regulation, or will have to add water treatment to support their use. At least review and sign off by a licensed and bonded engineer might be a workaround for some of the potential liability. Water laws, rights and management can be a highly contentious issue.