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The Yodo River flows through urban areas and is typical for Japan in that its water is recycled. The three water works are on the lower reaches of the river. One task of the water works is to examine water samples for Cryptosporidium parvum and Giardia intestinalis (lamblia). This study examined raw water sampled at three water treatment plants of Osaka Prefectural Water Works for these organisms every month from December 1999 to March 2001. In addition, water was sampled summer and winter at 28 locations in the watershed of the Yodo River for the pinpointing of the sources of these microorganisms. There were more raw-water samples containing one or both of the organisms in winter than in other seasons. Of the 48 samples, 19 (40%) contained C. parvum; the maximum number of oocysts was 14/10 liters. The mean number of oocysts for all samples was 1.7/10 liters. In the watershed samples, detection rates for both organisms were greater in winter than in summer. Twenty (71%) of the 28 winter samples contained C. parvum; there was a maximum of 32 oocysts/10 liters, and the winter mean number of oocysts was 5.1/10 liters. These values for G. intestinalis were 23 (82%) of 28, 380 cysts/10 liters, and 40 cysts/10 liters, respectively. Many cysts and oocysts of these species were detected at four watershed locations along four tributaries receiving effluents from different sewage treatment plants. These catchment areas were residential zones where most households have a septic tank. Waste from the livestock industry was not a factor, as livestock are not kept in the area. Includes 8 references, figures.