some macrofaunal invertebrates like bivalves are filter feeders which accumulate toxins from the water. Looking at pollutant load of these organisms can give you an insight on the water quality .

Cassandra, there are lots of literature on bioindicators for rivers....may be reading this one will open up your scope....

Cloern, J. 2001. MEPS, http://www.int-res.com/articles/meps/210/m210p223.pdf

An increase in some macroinvertibrates, such as Trichoptera, Diptera, Oligochaeta, and Amphipoda can indicate an increase in pollution, particularly fertilizer runoff

Source:

Neumann, M. 2002. http://www.audiogolf.de/mneum/pdf/MN_2002_EI_2_379_399.pdf

Reduction in macro-invertebrate diversity and the resultant increase of opportunistic species like Chinoromus larvae is also an indication of incidence of pollution.

Cassandra, aquatic invertebrates have a huge species richness that offers a wide spectrum of environmental responses. Each species has a tolerant range to different environmental conditions.

Bonada 2006 http://biocenosi.dipbsf.uninsubria.it/didattica/Ecologia/Articoli/2006%20Bonada%20et%20al.pdf

Number of species is a great starting point.  Indices that include the diversity of mayflies are also effective.  EPT richness for example.  If you have solid ID skills then you can get into the tolerance values assigned to various macroinvertebrates...these work a lot better if you are IDing past family.

Have fun

Respiration strategy (e.g., tracheal gills, respiratory siphon, plastron, etc) is one crucial characteristic that plays into tolerance. Polluted waters are often low in oxygen and the adaptation of the organism for utilization of available O2 is important to focus on and is one of the main reasons EPT taxa are distinguished from other taxa when assessing water quality.