A methodology is described in which algae, Protozoa, bacteria and other microorganisms are identified and counted using relative abundance scales. Arguments for and against these scales are examined but their use is considered justifiable on economic grounds. Canonical correlation is evaluated as an analytical tool for relating the distribution of micro-organism groups to water chemistry variables. Three river systems in north-west England are investigated using this technique. In the Ehen, nitrite, phosphate and flow appear to relate to the distribution of diatoms, nonmotile green algae and filamentous algae. Although there is a tip leachate problem with high iron concentrations, the correlation does not identify iron as a significant variable. For the Derwent, phosphate and biochemical oxygen demand relate to the distribution of most groups except the blue-green algae. For the nutrient-poor Irt, physical, rather than chemical, variables are important.