the basic physico-chemical analysis, you may analysis subject to dissolved oxygen, oxygen demand either biological or chemical, suspended solids, nutrient, ionic species
For further analysis, you can extend to hydrocarbon, pesticide, metals, or even new emerging pollutant issue like pharmaceutically active compounds analysis
There are a number of water quality parameters that can be used for assessing water quality conditions. These parameters (or indicators) can be put into three groups: 1) chemical (for instance, pH, DO, BOD, COD, level of various inorganic and organic pollutants, dissolved or particulate), physical (for instance, temperature, turbidity, TSS, etc), and biological (for instance, fecal coliform, E. coli, and other water-borne bacteria and viruses). It is however important to understand that these indicators alone cannot fully answer the question whether a water body is "health" or not. In the United States, assessment of the "health" of water bodies depends on their “designated uses”. For instance, a water body may be designated for swimming or for fishing or for drinking water, whereby different setting criteria will be made. You can learn more about water quality standards at US EPA’s webpage http://water.epa.gov/scitech/swguidance/standards/
It would be important to define first what is meant by river "health", and what the desired water quality goals are. In addition to the metrics described previously, physical habitat assessments can also be conducted to infer water quality status based on the presence (or absence) of specific aquatic biota. Best of luck!
The health of urban river strongly correlates to health of the whole urban catchment (imprevious areas, types of surfaces, precipitation periodicity/intensity and many more). So I agree with professor Hubbart, it is important to define "river health" esp. whether you mean biological, chemical, physical conditions of stream or you want to assess the whole stream system holistically. I wish you all the best!
I would agree with Dr Lepeske. On top of the chemical, physical, and biological indicator, it would be interesting to assess/infer the water quality status by identifying the presence or absence of specific aquatic biota. Cheers..
Here is a recent article that outlines a rapid Physical Habitat Assessment method, that may be of some use. Hope your work is going well.
Hooper, L., and J.A. Hubbart. 2016. A Rapid Physical Habitat Assessment of Wadeable Streams for Mixed-Land-Use Watersheds. Hydrology, 3(4), 37; DOI: 10.3390/hydrology3040037
Article A Rapid Physical Habitat Assessment of Wadeable Streams for ...