Transport of Cryptosporidium parvum oocysts and Giardia lamblia cysts in the aquatic environment is poorly understood. Information about their transport is essential for actual risk assessment and development of effective control practices. Several studies have suggested that attachment to soil particles is not likely to occur, but the hypothesis has not been well tested, partly because enumeration of C. parvum oocysts or G. lamblia cysts [written as (oo)cysts] in the presence of soil has been difficult. In this paper, a combination of flow cytometry, and epifluorescence and confocal microscopy was successfully used to enumerate (oo)cysts in the presence of soil and determine whether (oo)cysts travel freely in water or attached to soil particles. The maximum soil concentration in water samples for reliable enumeration of (oo)cysts was 2 mg/L. Particle attachment experiments detected attached pairs of oppositely charged beads and (oo)cysts, while no attachment was observed between like charged beads, (oo)cysts, and soil particles. These results support the hypothesis that electrostatic forces govern the interaction between (oo)cysts and soil particles. Batch experiments further confirmed the null hypothesis (p > 0.05) that (oo)cysts do not attach to natural soil particles. These findings suggest that, when (oo)cysts have been entrained in overland flow (i.e., runoff), they will travel freely in the water and not as part of the particulate sediment load.