January 2023

How do Environmental Factors Affect Microbial Groundwater Quality in Uganda and Bangladesh?

This research brief summarizes the 2020 publication by Poulin et al. in Environmental Science and Technology, entitled “What Environmental Factors Influence the Concentration of Fecal Indicator Bacteria in Groundwater? Insights from Explanatory Modelling in Uganda and Bangladesh”.


Groundwater, or water found below the earth’s surface, accounts for more than 97% of the world’s freshwater resources (Mullen 2022). Groundwater often supplies agricultural, industrial, and domestic water users, especially for those living in rural areas who cannot access water through piped networks. Despite being relatively more protected than open surface water bodies, groundwater remains prone to microbial contamination due to various factors, such as geological context, human and animal presence, sanitation systems, land cover, runoff, flooding, and climate (Figure 1). The concentration and persistence of microorganisms from human and animal feces is influenced by these factors.

This study sought to understand how different environmental factors influence fecal indicator concentrations in groundwater. It included two countries, Bangladesh and Uganda, which differ in their population density, topography, water, sanitation and hygiene (WASH) infrastructure, and rainfall. Data from satellite imagery, census data, and hydrological models allowed us to investigate the relationships between these environmental risk factors and microbial water quality of groundwater supplies. Our goal was to provide decision-makers with a framework for identifying contamination-prone areas using remote information and prioritizing water safety management efforts.

Groundwater Contamination


Lake in Uganda


  • We examined untreated drinking water sources from groundwater in 48 out of 136 districts, a wide geographic coverage.

  • To assess the level of fecal indicator bacteria (FIB; a group of organisms suggestive of fecal contamination), we obtained georeferenced data from three organizations: Water and Health for All (125 water sources), Whave (3,010 water sources), and Water Mission (240 water sources). The combined data from three organizations resulted in 3,375 microbial water quality test results collected over a period of eight years (2010−2018) from groundwater sources such as boreholes, tube wells, and springs.


  • We examined untreated drinking water sources from groundwater in only two of eight divisions in Bangladesh, representing a portion of the country.

  • We obtained georeferenced data on microbiological groundwater quality from the WASH Benefits trial (WASH Benefits n.d.; Ercumen et al. 2018). These data included 1,638 microbial water quality tests conducted between July 2013 and April 2014 on deep tube wells.
River in Bangladesh

Discussion and conclusions


Detectable fecal contamination in Uganda (52% of water sources) was higher than in Bangladesh (25%), possibly due to the geological differences between the two countries. Aquifers in Uganda consist of fractured rocks and weathered mantles. Bangladesh’s aquifers are composed of sediments like silts, clay, and sand, which require more time to transfer bacteria from the surface to underground water reserves. Due to this, Uganda’s groundwater resources are likely more vulnerable to microbial contamination.

Water well

According to previous research, shallow groundwater sources such as springs and dug wells are more prone to fecal contamination than deep sources such as tube wells and boreholes. In this study, we sampled both deep and shallow water sources from 308 boreholes (83%), 48 springs (13%), and 15 dug wells (4%) in Uganda and only deep tube wells in Bangladesh, which may have contributed to the higher prevalence of fecal contamination found in Uganda in this study.

47% of the Bangladeshi population has access to basic toilet facilities, compared to only 19% in Uganda (Prüss-Ustün et al. 2019). This further explains why shallow groundwater was prone to fecal contamination in Uganda.


In Uganda, anthropogenic activities were associated with higher fecal contamination: water sources were more prone to contamination if they were located in areas with higher population, higher cropland coverage, lower forest coverage, or higher livestock density, or if they were nearer to a city.


In Bangladesh, higher contamination levels typically occurred in areas with more limited human activities, signified by lower artificial land cover, lower cropland coverage, and higher forest coverage. This showed that anthropogenic activities are not associated with source water contamination in Bangladesh. Prior studies have shown that latrine density and domestic animals are the main sources of water source contamination in Bangladesh (van Geen et al. 2011); however, our results showed high contamination in forested areas, suggesting wildlife or open defecation practices may have contributed to higher FIB.

This study demonstrates how the environmental data, such as those provided by satellite imagery, can provide insight into groundwater contamination risks. Analyses across two different geographic areas (Uganda and Bangladesh) illustrate that risk factors vary across contexts for multiple reasons. Accordingly, decision-making related to water safety management should rely on data and analyses specific to the particular geographic area of interest.

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