Safe drinking water is a top priority in preventing disease outbreaks and is of general concern to everyone. This study examines the occurrence of Cryptosporidium and Giardia in Hungarian drinking water supplies for the first time. A total of 76 raw and drinking water samples were examined using the U.S. EPA Method 1623. From these 15 of 34 (48.4%) raw water samples tested positive for Giardia and 7 (26.6%) for Cryptosporidium. Twelve of 45 (26.7%) drinking water samples were positive for Giardia and 6 (13.3%) for Cryptosporidium. Overall, Giardia cysts and/or Cryptosporidium oocysts were detected in 48% of the raw water samples and 35% of the drinking water samples. The highest levels in drinking water were found to be 3 oocysts/100 litres of Cryptosporidium and 63.6 cysts/100 litres for Giardia, enough to cause giardiasis. The highest levels in raw water were 1,030 cysts/100 litres for Giardia and 50 oocysts/100 litres for Cryptosporidium and higher oocyst densities were associated with source water receiving effluents from sewage treatment plants or originating from a forest environment. In addition to this monitoring, riverbank filtrated water and raw water from the River Danube in Budapest were monitored in order to ascertain protozoan removal efficiency of riverbank filtration (RBF). A total of 157 samples, including 87 samples from the River Danube and 70 samples post RBF, were examined. Cryptosporidium and Giardia were detected regularly in the river water but never in riverbank filtered water suggesting the effectiveness of RBF as a purification method. The occurrence of Cryptosporidium oocysts and Giardia cysts in the investigated water supplies may require the water utilities and water authorities in Hungary to apply additional monitoring and treatment and/or watershed controls.