In this study, we aimed to assess the geographic inequalities in access to improved water and sanitation facilities among Nepalese households. We conducted this study based on cross-sectional data obtained from Nepal Demographic and Health Surveys. The quality of water sources and sanitation were defined by World Health Organization (WHO) guidelines. The geographic categories used in the analyses included developmental region, ecological zone, and urbanicity. Percentages of households having access to improved toilet (5.6% in 1996 vs. 40.5% in 2016) and water (19.3% in 1996 vs. 27% in 2016) facilities has been increasing steadily since 1996 with a great proportion of the households still lacking access to these services. The number of households sharing the same toilet and traveling time to reach water sources have also decreased at the same time. Households in Far Western and Mountains had the lowest odds of having access to improved toilet and water facilities. Noticeable progress has been achieved in improving WASH (water, sanitation, and hygiene) coverage at national level, however, it is uneven across developmental and ecological zones. Households in the Far Western and Mountain regions appeared to be the most geographically disadvantaged in terms of having access to improved water and sanitation facilities.