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<i>Cryptosporidium</i> and <i>Giardia</i> are two water- and foodborne protozoan parasites that can cause diarrheal diseases. Poor microbial quality, sanitation conditions, and hygiene practices at exposure to biogas wastewater are important risk factors for human and animal infection. This study highlights the presence and level of both parasites in the environment in relation to biogas waste reuse in Vietnam. A total of 239 samples were collected from different types of samples in the studied districts in Bac Giang province in 2020 via direct immunofluorescent detection to study the occurrence of <i>Cryptosporidium</i> spp. and <i>Giardia</i> spp. (oo)cysts. Among the samples, <i>Cryptosporidium</i> was found in 19 (7.9%) with concentration from 1.10⁴ to 3.10⁵ oocysts/100 mL, while <i>Giardia</i> in 40 (16.7%) with concentration from 1.10⁴ to 2.10⁶ cysts/100 mL, respectively. In detail, the results show that the percentages of positive detection of <i>Cryptosporidium</i> spp. and <i>Giardia</i> spp. in influent, effluent, sewage canal, and vegetables were 13.1% (11/84), 6.0% (5/83), 15.4% (2/13) and 5.9% (1/17) and 26.2% (22/84), 7.2% (6/83), 7.7% (1/13) and 5.9% (1/17), respectively. The results show a trend of decreasing <i>Cryptosporidium</i> and <i>Giardia</i> densities, without statistical significance. Although these parasites decreased after biogas treatment, the remaining loads observed in biogas effluent can reach the watercourses and soil receiving it. Further investigations are needed to contribute to a general understanding of the risk of protozoan parasites, as well as strategies to control and reduce the contamination of environmental water sources and plants and reduce the burden of the pathogens in biogas wastewater in Vietnam.