Globally, nearly 1.7 billion cases of diarrhea occur among children under five every year. In Africa it accounts for over 70% of the under five mortality, while in Kenya it remains among the leading cause of mortality and morbidity among under-fives. The study was meant to determine the factors associated with diarrheal conditions among under-five children and health systems performance in Migori County; to determine the effects associated with diarrheal conditions among under-five children and health systems performance in Migori County and to establish the prevention and control strategies associated with diarrheal conditions among under-five children and health systems performance in Migori County. A mixed method approach was used and a total of 334 children under five were sampled using cluster sampling techniques. Descriptive and inferential statistics were generated during data analysis. The findings revealed that factors including latrine ownership (p < 0.001); type of latrine (p = 0.003); presence of flies on latrine (p= 0.005); practicing Open Defecation (p = 0.006); time used to fetch water (p = 0.016); distance to water source (p = 0.007); main source of income (p = 0.028); household monthly income (p = 0.015) and wealth index (p = 0.039) had an influence on occurrence of diarrhea in under five children. Stunting growth (p = 0.007); reduction in cognitive development (p = 0.012); severe wasting (p = 0.043); dehydration (p = 0.028) and financial losses (p = 0.004) were found to be significant effects of diarrhea. Protection of water sources (p < 0.001); container for collecting water (p = 0.006); type of container for storing drinking water (p = 0.007); treatment of water at the point of use (p = 0.004); methods of water treatment (p = 0.003); methods of infant feces disposal (p = 0.016); methods of food storage (p < 0.001) and rotavirus vaccination (p < 0.001) were found to be significant prevention strategies for diarrhea. Bivariate analyses revealed that, factors such as latrine ownership (p = 0.003); presence of flies on latrine (p = 0.005) and practicing OD (p = 0.006) were significant in predicting the outcome. The significant effects which predicted the outcome on bivariate analyses were stunting growth (p = 0.009); reducing cognitive development (p = 0.007); dehydration (p = 0.018); financial losses (p = 0.023) and productivity losses (p = 0.014). Finally the prevention strategies consisting of protection of drinking water source (p = 0.014); treatment of drinking water at POU ((p = 0.015); methods of food storage (p = 0.024) and rotavirus vaccination (p = 0.003) were significant in predicting the outcome. Regression analyses the factors, effects and prevention strategies had significant prediction performances of X2(3, N=334 = 19.75, p=0.003), X2(5, N=334 = 11.36, p=0.005) and X2(3, N=334 = 22.02, p=0.004) respectively. They further (factors: R2 = 0.826), (effects: R2 = 0.862) and (prevention strategies: R2 = 0.893) proved that they were significantly good predictors of the outcome variable. The Study concluded that diarrheal factors, the effects and prevention strategies significantly predicted the response variable. There should be focused community-based identification of factors attributing to diarrhea and locally addressing them. Earlier management of the effects of diarrhea should be prioritized. Further the county should embrace community health strategy by strengthening prevention strategies through the design of county specific comprehensive diarrhea prevention and control network and framework.