Amoebiasis is a primarily zoonotic disease, mainly transferred through the fecal-oral route and waterborne. Amoebiasis is still a big challenge for human and animal health and is a major cause of diarrhea in developing countries, including Ethiopia. Therefore, the study was conducted to assess the epidemiology of the disease in humans, dogs, and the occurrence of the parasite in water bodies. A prospective cross-sectional study was conducted in selected districts of the Bale zone in southeastern Ethiopia. Pet owners were selected randomly. Socio-demographic data were collected using a questionnaire and fecal samples were used to perform microscopic examination. A total of 383 fecal samples of humans, 383 fecal samples of dogs, and 58 water samples were studied from December 2019 to July 2020. Of 383 humans, 179 were males and 186 were females, while 94 individuals were grouped as children younger than 8 years, 164 were grouped as youth within the age range of 8-18 years, and 125 were grouped as adults who were older than 18 years. Of 383 local breeds, dogs were grouped as 87 puppies younger than one year, 192 young dogs with the age range of 1-2 years, and 104 adult dogs who were older than 2 years. Fecal samples were taken from 173 male and 210 female dogs. The water samples were taken randomly from the water sources (river, lake, pond, or water tank) at different sites where dogs and humans can easily contact water to use for different purposes. Of the total samples, 70 humans (18.3%), 63 dogs (16.5%), and 16 water samples (27.6%) were contaminated with the parasite. The major risk factors for the transmissions of parasites were contaminated drinking water, large family size, open-air defecation, and improper handwashing. The present study revealed that the human reservoir was a major risk factor for the spread and transmission of amoebiasis in dogs. The high prevalence of the disease might be due to open-air defecation, unhygienic health practices, domestic animals inside the houses, and using local water bodies as a drinking source.