Well the first way to tell is by visual inspection. Look to see if the area around the pond is disturbed in any way ie. animal prints etc. In addition to that you could take a sample in a glass jar and visually inspect for life in the water. If the ripples that you describe are occurring without rain or wind particulates falling into the pond then they are probably produced by insects or aquatic species.
Anytime and anywhere there is a dark, murky pond, you can bet there are raccoons using it as a water source. All such ponds will also be host to mosquitoes and other insect species. Likely, too, there will be algae and other aquatics. And microbiological activity is a given. You don’t need to “test” to be sure of the latter, but if you are curious to know what is there, take a sample and send it to an extension agency.
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