Two classes of parasites with an environmental stage in their lifestyle have recently emerged as significant gastrointestinal pathogens for humans. Microsporidia represent a group that contains a number of genera related to the genus Cryptosporidium. They are generally transmitted via direct human to human contact, but can survive in water and food, and recently have been found in surface water used as drinking source water. Their most common host range is in patients with clinical AIDS. Limited work to date suggests the group is susceptible to chlorine achievable CxT (concentration x time) values and is coagulated by filtration. Cyclospora cayetanensis is a species of parasite that has caused outbreaks from contaminated food. Its major risk is from the use of inadequately treated water used for irrigation. Cyclospora can infect normal and immunosuppressed hosts. Current information regarding the lifestyle, transmission, and control of both groups of parasites are discussed, with a health risk assessment analysis.