There are microscopic crustaceans called copepods. They can be found in both freshwater and saltwater, as well as moist moss, puddles collected in leaves, and even in humans. They range in size from .5mm to 2mm.
There are zooplankton and phytoplankton. Phytoplankton are basically plants that are microscopic and are necessary for the freshwater ecosystem to survive. Zooplankton are also microscopic organisms but are more like animals in that they cannot produce their own food. There are literally millions of individuals that fit within these categories, so it would depend on the specific freshwater ecosystem you were asking about.
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