First off, without knowing the specifics, it is very hard to say, but in general, so long as you are careful and don't ingest (i.e. drink) or breathe in aerosols/droplets of the water, it should be OK. Washing your hands and spraying down work surfaces with hand sanitizer after you finish your observations is a good idea too. The risks probably aren't substantially greater than digging in the soil in your garden. Other standard lab practice is also a good idea - don't eat/drink/smoke/apply lip gloss/makeup while doing this, keep your hair tied up, clean up spills immediately, keep your hands off/away your face.
What is in the water strongly depends on your water source. If you got it from the local duck-pond, it could contain all sorts of things associated with bird faeces, such as Avian botulism, Salmonella, Cryptococcosis and Histoplasmosis (though these last two are more associated with soil than water), even viruses, such as avian influenza, though you'd only likely get this by handling sick birds or the feces directly.
Water that runs off a farm, might have a range of bacterial species, such as E. coli, and Brucella, as well as eukaryotic pathogens such as Giardia, Pinworms (we carry these too, 30-60% of children has these at any given time) and a whole range of other parasites.
Water from a puddle in your back-yard, on the street, or an actively flowing stream (collect the water from a still-water spot) is less likely to contain parasites that might harm you, but bacteria will remain in suspension. Again it depends on source - the neighbour's (or your) cat/dog can carry pinworms, tapeworms, even Toxoplasma, as well as a range of bacteria similar to those listed for the farm above. Any wild animal that visits your place can also carry a range of things.
the highest risk places are areas with a lot of people. We carry a huge range of native and non-native pathogens that you can pick up from people's dirty habits and leavings. These include bacterial species (E. coli again, but also several others), viruses such as norovirus and rotavirus, and the aforementioned parasites. However, you are much more likely to catch these sorts of things from shared facilities such as toilets rather than water, unless you are collecting from a high-traffic area such as a popular forest walk which doesn't have toilet facilities nearby.
These are the worst-case scenarios, follow good hygiene practices and good laboratory practice and you should be fine.