Lack of safe water, poor hygiene and sanitation accounts for about 90% of the diarrheal diseases in the world. Globally, half a million people lack adequate sanitation, leading to fatalities for above five million people annually. This study examined the sanitation risk factors associated with childhood diarrhea in Igembe South Sub County in Meru County. The objectives of the study were; to establish the sanitation etiological causes of diarrhea, identify the distribution of diarrhea cases, identify the household sanitation risk factors contributing to diarrhea, assess household water and hygiene practices, and analyze the microbial contamination of water sources in Igembe South Sub County, Meru County. A retrospective and cross sectional study was carried out in Nyambene Sub County Hospital, Igembe south Sub County for the period December 2022 to March 2023. The sample size was 196 children. Data for the under five years children treated for diarrheal diseases was collected from both inpatient and outpatient department. Thereafter, the guardians and care givers were followed up in their homes where sanitation indicators were collected through a structured questionnaire and observations. Water samples were collected from communal and individual water sources from every ward, for microbial analysis. Data was analyzed by use of SPSS version 24 and ANOVA, inferential statistics was done and presented in figures and tables. There was a significant relationship between cases of diarrhea in children below five years and shortage of household latrines. There was also a positive significant relationship (p=0.0034) between the diagnosis made and the sanitation risk factors (hand washing and source of household water). Besides, sanitation related factors were reported to significantly influence the prevalence of diarrhea among children below 5 years; hand washing before preparing the baby’s food (p = 0.048) and source of household water (p = 0.042). The study established that the predominant sanitation etiological cause of diarrhea in children under five years in Igembe South was E. histolytica (65% (n=13)). Besides, 75.5% (n=148) of the children in the Sub County diagnosed with diarrhea were partially immunized, and 55.6% (n=109) of children below five years with diarrhea in Igembe South Sub County were residents of Amwathi and Kiegoi Antubochiu wards. The study also revealed that more than 43% (n=84) of the households did not have a hand washing facility. The water samples from three sources tested positive for E coli contamination. Ura River, Mwamba River, and Muura River were unfit for human consumption,as they were grossly polluted (category D). Kanuni ward whose larger population (34.2%) depend on Ura river is the mostly affected. The study concluded that the predominant sanitation etiological cause of diarrhea in children under five years in Igembe South was E. histolytica which is prevalent in the contaminated rivers in South Igembe SubCounty. Basic sanitation is paramount in ensuring hygienic excreta disposal and a clean and healthful environment within the households. Availability of safe drinking water, can significantly reduce diarrhea episodes in children under five years. The County Government of Meru should closely monitor proper use of sanitation facilities and safety of water sources in all wards, to ensure that each household has basic sanitation facilities.