The achievement of sustainable and lasting effects from projects is a significant challenge for donors and the agencies implementing and supporting water supply in developing countries. The current estimations for Sub-Saharan Africa (SSA) suggest that only two out of three water points in rural areas on the continent are functioning at any given time. The region of SSA includes many of the world’s poorest countries, and sustainability of water supply services is vital concerning people without access to safe drinking water. Not surprisingly, many policies and planning decisions are taken without access to adequate data, a situation that increases the risk of inappropriate measures being adopted. The objective of the present study is to address the potential of applying geospatial technology to monitor the sustainability of rural water supply services. It focused on the Wami River Basin in Tanzania due to its diversified use, which benefits a multi-diversity of stakeholders and its role as a vital area for providing water, food and other natural resources. It is in the interest of this study to understanding reasons for “success” and “failure” of water points using Geographic Information Technologies (GIT) based approach to analyse factors of biophysical and human domains that respond to both in time and space. The study analyses the trends in annual and seasonal rainfall time series in the Wami River Basin during 1983–2017 for any significant changes in the patterns and how they affect the access to water supply services in rural areas. First, waterpoint mapping datasets were analysed considering seasonal variation. Later, the study focused on changes in land-use/land-cover patterns upstream and downstream and explored the spatial econometric technique by analysing the impact of land-use/land-cover change on water ecosystem services for domestic use in the basin. Lastly, I provide my vision of the water-food-land nexus giving attention to how it relates to agriculture expansion. I identify trade-offs between and assess the synergies associated with the influence of agriculture intensification and anticipation of water services concerning data availability. The results showed that water points were significantly affected by seasonal changes, both in terms of availability and water quality. There also exists a strong relationship between rural water services and seasons. With a time series of maps, change analysis can reveal the overall development of the land distribution, including the detection of sites of different types of changes. In general, net gain and net loss were observed downstream, indicating that this region was more affected than upstream. I found that all measured land-use/land-cover changes and water point characteristic correlations were statistically significant; therefore, I concluded that land-use/land-cover change affects the water ecosystem in the basin. These findings provide baseline information for decision-makers and stakeholders concerning water supply services for better planning and management decisions in the basin. Furthermore, the approach has contributed to the application of geospatial technologies in rural water supply services and might help pursue sustainability strategies in other basins. The approach based on detailed large-area field data to identify variations in the spatial distribution of the water service supply regarding quality and quantity to a reasonable degree of accuracy. Hence, it presents an excellent opportunity to provide relevant information about water supply services performance in response to spatially and temporally critical importance. However, due to the lack of up-to-date information, it does not cover other essential access aspects concerning the vulnerability of the water services like lack of financial and governance components that play a significant role in the sustainability of rural water supply services. Therefore, more studies should be undertaken to explore the use of Remote Sensing (RS) and Geographic Information Systems (GIS) with different temporal and spatial scales in future research, integrating institutional and socio-economic analyses of environmental sustainability.