A total of 383 groundwater samples from 166 different sites were analyzed for Cryptosporidium, Giardia, and other microbiota (1-500 um) using immunofluorescence assay and light microscopy procedures. Analysis of the data showed 11% of the sites (19 of 166) were sometimes positive for Cryptosporidium and/or Giardia. 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, amebae, 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 gave no better prediction of the pathogens than the three general categories. In making the determination of vulnerability to contamination, priority should be given to those groundwater sources with a diversity of microbiota. Includes 9 references, tables.