Waterborne parasitic diseases form one of common and important public health and economic problems in low- and middle-income countries, though little is known on the burden and patterns of these diseases in most regions. This systematic scoping review informs on the prevalence and pattern of waterborne parasitic infections in eastern Africa from 1st of January 1941 to 31st of December 2019. The review found limited number of published studies on waterborne parasitic diseases, though 13 of the 15 studied countries in eastern Africa provided one or more published report(s) totalling 47 reports. Focus of studies was mainly on schistosomiasis where 44.8% of the 47 retrieved studies reported it. Other frequently reported diseases were giardiasis (23.4% of reports), soil-transmitted helminths (23.4%) and amoebiasis (21.3%). Rarely reported diseases were malaria, cryptosporidiosis, isosporiasis, dracunculiasis and trichomoniasis. Based on parasitological examinations, schistosomiasis prevalence ranged from 17 to 33% in Burundi, 1.9 to 73.9% in Ethiopia, 2.1 to 18% in Kenya, 7.2 to 88.6% in Uganda, 22.9 to 86.3% in Tanzania, 27.2 to 65.8% in Somalia, 15 to >50% in Mauritius, 2.4% in Eritrea and 5.0 to 93.7% in Madagascar. Amoebiasis prevalence was 4.6–15,3% (Ethiopia), 5.9–58.3% (Kenya), 54.5% (Rwanda), 0.7–2.7% (Sudan), 19.93% (Uganda) and 4.5–5.0% (Seychelles). Giardiasis prevalence was 0.6–55.0% (Ethiopia), 16.6% (Kenya), 3.6% (Rwanda), 21.1% (Sudan), 40.7% (Uganda), 45.0% (Eritrea) and 3.3–6.0% (Seychelles). Soil-transmitted helminths prevalence was 41.7–52.4% (Ethiopia), 32.4–40.7% (Kenya), 9997 cases (Rwanda), 85.0% (Somalia), 4.7% (Madagascar) and 1.1–84% (Seychelles),
Ascaris lumbricoides
,
Trichuris trichiura
and hookworms were the most common helminths detected. Malaria prevalence was 2.9–4.31% (Ethiopia), an annual episode of 9 million people (Sudan), 13.0% (Tanzania), 146 hospital cases (Madagascar), 1.4–2.0% (Seychelles) and <5.0% in Djibouti. It is also observed that >50% of the populations in eastern Africa region lack improved drinking water sources or sanitation facilities. This may account for the observed high prevalence of the diseases. The author also suggests likely underestimation of the prevalence as most waterborne parasitic diseases are neglected and cases likely only recorded and left unpublished in health facilities. Thus for a thorough mapping of burdens of these diseases, grey literature, including hospital records must be reviewed while interventions focusing on improved water and sanitation are likely to reduce the burden considerably.