Your river classroom sounds like a fantastic resource! It's really wonderful that you're making use of the river with your middle school students. I can point you in a few different directions for sampling for bacteria.
We test water samples for bacteria here in Royalton using the IDEXX Colilert system. It's a 24hr test recognized by the EPA and used widely in water quality testing. In short, in the test we add colilert reagent to a 100mL water sample, incubate it for 24hrs in a specially sealed tray and then read the sample using a UV light. Samples that are positive for E.coli fluoresce under the light and we can quantify how much E.coli is present based on the portion of the tray that is fluorescing. We have 5 samples worth of reagent left at this point and would be happy to run samples if you can get them to us. There are pretty tight time limits for the samples to be considered valid (they need to be processed within 6 hrs), which may make that difficult.
You might consider contacting Jenna Guarino, a watershed education consultant with Ecotone Education here in Vermont, that we've worked with and who has done some water quality work using petri dishes in the past. She's a great resource and I'd be happy to connect you. Jenna developed many of the materials that we use with school groups (available at http://
There may also be some folks at the Agency of Natural Resources, Department of Environmental Conservation who may be good resources. Jim Kellogg comes to mind, he supervises macroinvertebrate sampling for the state and also is the contact for a program called the LaRosa program, which among other things tests water samples for bacteria. I'm not sure if the state would be able to help you out by running samples, but I'd be happy to connect you with them if it would be helpful.
Let me know if I can be of help or if you'd like to talk in more detail about any of these options. Good luck!