Analysis of groundwater for the presence of microbiota offers researchers a way to estimate the potential for Giardia and Cryptosporidium contamination.A total of 383 groundwater samples from 166 different sites were analyzed for Cryptosporidium, Giardia, and other microbiota (1–500 μm) using immunofluorescence assay and light microscopy procedures. Analysis of the data showed 11 percent of the sites (19 of 166) were sometimes positive for Cryptosporidium, Giardia, or both. Statistical analyses determined that microbiota in eight major groups were indicative of Cryptosporidium and Giardia contamination. These groups include algae, arthropods, rotifers, fungi, nematodes, colorless flagellates, amoebae, and gastrotrichs. Cryptosporidium and Giardia occurrence also correlated positively with the three risk categories developed by the US Environmental Protection Agency to rank direct surface water influence on groundwaters (p = 0.001). However, the specific numerical scores used to determine risk categories provided no better prediction of the pathogens than the three general categories. To determine vulnerability to contamination, researchers first should investigate those groundwater sources with a diversity of microbiota.