Recharge Estimates Research Articles

Evaluation of Climate Change Impact on Groundwater Recharge in Groundwater Regions in Taiwan

Climate change can directly or indirectly influence groundwater resources. The mechanisms of this influence are complex and not easily quantified. Understanding the effect of climate change on groundwater systems can help governments adopt suitable strategies for water resources. The baseflow concept can be used to relate climate conditions to groundwater systems for assessing the climate change impact on groundwater resources. This study applies the stable baseflow concept to the estimation of the groundwater recharge in ten groundwater regions in Taiwan, under historical and climate scenario conditions. The recharge rates at the main river gauge stations in the groundwater regions were assessed using historical data. Regression equations between rainfall and groundwater recharge quantities were developed for the ten groundwater regions. The assessment results can be used for recharge evaluation in Taiwan. The climate change estimation results show that climate change would increase groundwater recharge by 32.6% or decrease it by 28.9% on average under the climate scenarios, with respect to the baseline quantity in Taiwan. The impact of climate change on groundwater systems may be positive. This study proposes a method for assessing the impact of climate change on groundwater systems. The assessment results provide important information for strategy development in groundwater resources management.

Eklenik Sapma Yaklaşımı ile Türetilen Yağış-Seviye İlişkisinden Yeraltısuyu Beslenimi Tahmin Modeli: Gazipaşa (Antalya) Ovası Akiferi Örneği

Groundwater recharge is one of the basic parameters required in water resources potential calculations. There are several methods applied to estimate groundwater recharge, however, every method has its own advantages and disadvantages, due to the fact that the theory of infiltration and the vadose zone hydrology is highly complex. Search for a method based on less complex theory, which requires readily available and representative parameters, and gives reliable results is still of interest. Groundwater recharge estimation based on the assumption that the groundwater level in the saturated zone rises as a result of the cumulative rainfall may well meet these expectations. It requires less data, easy to calculate and gives relatively reliable results. In this paper, following an explanation of the theoretical basis, the method is applied to Antalya-Gazipaşa plain aquifer. The analyses have revealed that the method can produce the deviations in observed groundwater based on the cumulative rainfall departure, with high coefficients of determination. The method was also used to analyse the external effects, such as percolation from river beds and groundwater pumping, on the deviations of groundwater levels from the average, which suggests that the plain aquifer constitutes an open system.

Groundwater recharge estimation using groundwater level fluctuation patterns in unconfined aquifer of Yogyakarta City, Indonesia

Water demand in the world increases rapidly every year, especially in urban areas due to population growth and improved economic conditions. The largest freshwater source on earth is groundwater that can be utilized and easily obtained. However, the number of groundwater resources is very dynamic, depending on the recharge and discharge, including groundwater extraction. Increasing groundwater abstraction will cause a decline in groundwater level and seawater intrusion in the coastal area. Groundwater level fluctuation trends can be used to estimate groundwater recharge for optimum utilization. Therefore, this study aims to find the trend of groundwater level fluctuation related to rainfall to estimate the groundwater recharge in Yogyakarta City, Indonesia. The study was carried out by measuring the groundwater level of four monitoring wells that spread evenly in Yogyakarta City from 2011 to 2017 every month and comparing the result to monthly rainfall and annual groundwater abstraction from hotels in Yogyakarta City. The annual trend of rainfall and groundwater level fluctuation analysis using the nonparametric Mann-Kendall test and analyzing the trend's magnitude using the nonparametric Sen’s method. The groundwater recharge was estimated by using the water table fluctuation (WTF) method. The study results showed that the trend of rainfall and groundwater level fluctuation is positive in the city's western and eastern parts. However, the groundwater level fluctuation in the city's central and southern parts is a negative trend due to groundwater over-exploitation by hotels. Groundwater recharge is estimated at around 158 up to 538 mm/year based on the WTF method. Higher groundwater recharge was identified in the city's central and eastern parts due to the high contribution from urban wastewater recharge.

Unpacking some of the linkages between uncertainties in observational data and the simulation of different hydrological processes using the Pitman model in the data scarce Zambezi River basin

AbstractThe main objective of this study was to use an uncertainty version of a widely used monthly time step, semi‐distributed model (the Pitman model) to explore the equifinalities in the way in which the main hydrological processes are simulated and any identifiable linkages with uncertainties in the available observational data. The study area is the Zambezi River basin and 17 gauged sub‐basins have been included in the analyses. Unfortunately, it is not generally possible to quantify some of the observational uncertainties in such a data scarce area and mostly we are limited to identifying where these data are clearly deficient (i.e., erroneous or non‐representative). The overall conclusion is that the equifinalities in the model are hugely dominant in terms of the uncertainties in the relative occurrence of different runoff generating processes, although water use uncertainties in the semi‐arid parts of the basin can contribute to these uncertainties. The identification of landscape features that suggest the occurrence of saturation excess surface runoff provides some information to constrain the model. Improved independent estimates of groundwater recharge is also identified as a key source of observational data that would help a great deal in constraining the model parameter space and therefore reducing some of the model equifinality.

Groundwater Recharge Estimation Using Water Budget and Water Table Fluctuation Method in the Jakarta Groundwater Basin

The Jakarta Groundwater Basin is one of the groundwater basins with the highest development, economic, and business activities in Indonesia. Groundwater damage has become a major growing issue in the Jakarta groundwater basin. Intensive development has led to the overuse of groundwater in this basin. Efforts are needed to manage, protect, and conserve groundwater in this basin to support the development and economic activities sustainably. Jakarta, as the capital city of Indonesia, is located in the groundwater basin. Groundwater sustainability is determined by the amount of groundwater recharge in those basins, so knowledge of groundwater recharge is important. Groundwater is an important part of a hydrological cycle, and groundwater recharge ensures groundwater sustainability in some areas. This study aims to estimate groundwater recharge in the Jakarta groundwater basin using the water budget and water table fluctuation method. The water budget method used is Thornthwaite, Dingman, and Edijatno-Michel. The Water Table Fluctuation methods used are Dellin and Delottier. Analysis of the amount of groundwater recharge estimation is carried out using the ESPERE Version 2 software. Output data is then further analyzed using descriptive and inferential statistical approaches to determine whether there is a difference in groundwater recharge amount based on the water budget and water table fluctuation. The results show that groundwater recharge based on water budget methods is 209–885 mm/year. The estimation of the largest amount of recharge was obtained using the Edijatno-Michel approach. The smallest amount of recharge was estimated using the Dingman-Hamon method. The average recharge of groundwater in Tanjung Priok is 305 mm/year, Kemayoran is 209 mm/year, and Bogor is 885 mm/year. Only 8–15 % of the annual rainfall that converted into groundwater recharge at the study area. Based on the analysis using the water table fluctuation method, groundwater recharge in this basin has a value of 240 mm/year. The variation of the amount of groundwater recharge is caused by the pros and cons of each method. Apart from that, geological factors, land use/land cover factors, and climatic variations in this basin can affect the research results. By considering the amount of groundwater recharge, groundwater management in the Jakarta groundwater basin needs to be carried out for harmonious development and groundwater conservation.

An Assessment of Groundwater Recharge at a Regional Scale for Sustainable Resource Management: Province of Alicante (SE Spain)

For decades, the Province of Alicante, located in the Southeast of Spain, has experienced important economic development associated with groundwater exploitation. The scarcity of superficial resources and irregular distribution in the time and space of rainfall, typical of the Mediterranean environment, together with the extensive limestone outcrops, have made groundwater a key resource for the area. However, insufficient knowledge about aquifers, especially the lack of precise recharge estimates, hinders regional water management. This study establishes updated recharge estimates and water budgets for the 200 aquifers found in Alicante, using readily usable methodologies and available data. These are soil water budget models, groundwater flow models, water table fluctuation methods, and spring flow analyses. The results show low mean annual values of recharge from precipitation (69 mm/year and a coefficient of 12%) and two main differentiated domains. The first one, in the northeast of the province, under more humid climatic conditions with larger carbonate aquifer systems, has higher recharge coefficients, ranging from 14% to 24%, and greater resources. For the rest of the province, where aquifers are smaller and annual averages of rainfall range between 250 and 400 mm, average recharge rates are low (9–12%).

Estimation of recharge in mountain hard-rock aquifers based on discrete spring discharge monitoring during base-flow recession

Estimation of aquifer recharge is key to effective groundwater management and protection. In mountain hard-rock aquifers, the average annual discharge of a spring generally reflects the vertical aquifer recharge over the spring catchment. However, the determination of average annual spring discharge requires expensive and challenging field monitoring. A power-law correlation was previously reported in the literature that would allow quantification of the average annual spring discharge starting from only a few discharge measurements in the low-flow season, in a dry summer climate. The correlation is based upon the Maillet model and was previously derived by a 10-year monitoring program of discharge from springs and streams in hard-rock aquifers composed of siliciclastic and calcareous turbidites that did not have well defined hydrogeologic boundaries. In this research, the same correlation was applied to two ophiolitic (peridotitic) hard-rock aquifers in the Northern Apennines (Northern Italy) with well-defined hydrogeologic boundaries and base-outflow springs. The correlation provided a reliable estimate of the average annual spring discharge thus confirming its effectiveness regardless of bedrock lithology. In the two aquifers studied, the measurable annual outputs (i.e. sum of average annual spring discharges) could be assumed equal to the annual inputs (i.e. vertical recharge) based on the clear-cut aquifer boundaries and a quick groundwater circulation inferable from spring water parameters. Thus, in such setting, the aforementioned correlation also provided an estimate of the annual aquifer recharge allowing the assessment of coefficients of infiltration (i.e. ratio between aquifer recharge and total precipitation) ranging between 10 and 20%.

Comprehending the groundwater recharge of a coastal city in humid tropical setting using stable isotopes

Unscientific urbanization in coastal cities has enforced the need for understanding groundwater recharge sources and processes for sustainable development. In this paper, stable isotope compositions of precipitation, groundwater and river water were determined to understand the significant recharge sources of phreatic aquifers in the two differently urbanized environments, viz. urban and peri urban clusters of Kozhikode District, Kerala, and southern India. The two monsoon systems viz., southwest and northeast, are the major source of groundwater recharge in the region, but due to change in landuse pattern in the last decade has significantly altered groundwater recharge. Hence with the aid of stable isotope ratios of water, estimation of point recharge of rainwater to the groundwater in different hydrgeological setting of the area was done. The monsoon rains contributed 35% in the urban alluvial aquifers, up to 39% in the urban laterite aquifer and 42% in the peri urban laterite aquifer. An attempt was made to correlate the landuse changes in the past decade in the region with the groundwater availability.

Estimating water balance components in irrigated agriculture using a combined approach of soil moisture and energy balance monitoring, and numerical modelling

AbstractInformation on water balance components such as evapotranspiration and groundwater recharge are crucial for water management. Due to differences in physical conditions, but also due to limited budgets, there is not one universal best practice, but a wide range of different methods with specific advantages and disadvantages. In this study, we propose an approach to quantify actual evapotranspiration, groundwater recharge and water inflow, i.e. precipitation and irrigation, that considers the specific conditions of irrigated agriculture in warm, arid environments. This approach does not require direct measurements of precipitation or irrigation quantities and is therefore suitable for sites with an uncertain data basis. For this purpose, we combine soil moisture and energy balance monitoring, remote sensing data analysis and numerical modelling using Hydrus. Energy balance data and routine weather data serve to estimate ET0. Surface reflectance data from satellite images (Sentinel‐2) are used to derive leaf area indices, which help to partition ET0 into energy limited evaporation and transpiration. Subsequently, first approximations of water inflow are derived based on observed soil moisture changes. These inflow estimates are used in a series of forward simulations that produce initial estimates of drainage and ETact, which in turn help improve the estimate of water inflow. Finally, the improved inflow estimates are incorporated into the model and then a parameter optimization is performed using the observed soil moisture as the reference figure. Forward simulations with calibrated soil parameters result in final estimates for ETact and groundwater recharge. The presented method is applied to an agricultural test site with a crop rotation of cotton and wheat in Punjab, Pakistan. The final model results, with an RMSE of 2.2% in volumetric water content, suggest a cumulative ETact and groundwater recharge of 769 and 297 mm over a period of 281 days, respectively. The total estimated water inflow accounts for 946 mm, of which 77% originates from irrigation.

A participatory approach to assessing groundwater recharge under future climate and land-cover scenarios, Tutuila, American Samoa

Study regionOceania, South Pacific, Polynesia. Study FocusChanging climates have the potential to significantly impact global water resources availability. On many volcanic islands, groundwater is the primary drinking water source, thereby making it essential to manage this limited resource carefully. In this study, we developed high temporal and spatial resolution groundwater recharge estimates for the Island of Tutuila, American Samoa using the Soil Water-Balance-2 (SWB2) model. Additionally, we predicted future recharge by running the calibrated model with combinations of dynamically downscaled general circulation climate model (GCM) predictions, and future land-cover scenarios developed collectively with local stakeholder groups. New hydrological insightsPresent-day results indicate 57 % of Tutuila’s rainfall becomes groundwater recharge, 8 % evaporates from the canopy, 15 % evapotranspires, and 20 % discharges as stormflow-runoff. Future climate scenarios suggest recharge may increase by 8 % or 14 % depending on global emissions. Land-cover was a less significant driver of hydrologic change, although increases in impervious surfaces showed a negative impact on recharge. This work is maintained as an active open-source project on GitHub, the world’s leading software development platform, thereby enhancing transparency, reproducibility, and participation from stakeholders and managers in American Samoa. This study is the first of its kind from a location within the South Pacific Convergence Zone, and provides insights into how human activities on global and local levels affect the future sustainability of essential resources.

Estimation of groundwater recharge using simulation-optimization model and cascade forward ANN at East Nile Delta aquifer, Egypt

Study regionThe Quaternary Aquifer at the Eastern Nile Delta (QAEND), Egypt. Study focusA novel model is studied to build relationships between the available geomorphological and hydrogeological data, and the unknown time-dependent recharge rates. This is useful in performing inexpensive sustainable simulation and management of the proposed aquifer. Recharge rates in the year 2005 are calibrated using the observed hydraulic heads. The unstructured grid version of MODFLOW (MFUSG) coupled with the Particle Swarm Optimization (PSO) algorithm is used to solve the calibration problem. Then, a multilayer Cascade Forward Artificial Neural Network (CFNN) is trained using the calibrated recharge rates to conclude the required relationships between available data and unknown recharge rates, for any subsequent year. Four different training methods are adopted for CFNN: 1) PSO, 2) Levenberg Marquart (LM), 3) LM in combination with the Bayesian Regularization (BR), and 4) hybrid algorithm between LM - BR and PSO, which is used for the first time in training the CFNN to predict the net recharge rates and is found to be the best one. New hydrological insights for the regionThe trained CFNN is used to provide the groundwater flow model, MFUSG, with necessary recharge rates during the transient simulation of the groundwater between 2005 and 2015. Good matching between simulated and observed hydraulic heads is validating the model in forcasting future recgharge rates.

Assessment of groundwater recharge along the Guarani aquifer system outcrop zone in São Paulo State (Brazil): an important tool towards integrated management

The quantification of the groundwater recharges represents useful and important information for water resource management. The volumes of infiltrated water are essential to maintain water storage in aquifers, as well as to the discharge of groundwater towards the rivers, especially in tropical areas. The outcrop zones of the Guarani Aquifer System (GAS) in Sao Paulo state (Brazil) are considered as their most important recharge areas; therefore, knowledge about recharge rates and processes is essential. They are also highly vulnerable to groundwater contamination, another important reason to protect them. This study aimed to estimate spatial and temporal variations of groundwater recharge in the mentioned GAS outcrop zones. Recharge rates were estimated using the Spatial Recharge (SR) method and then compared to other two traditional methods (base flow separation and water table fluctuation method). The SR method uses the spatial distribution of the evapotranspiration and rainfall from GLDAS and TRMM databases and the runoff after the Soil Conservation Service (SCS) empirical method. All three methods revealed similar estimates for groundwater recharge, ranging from 150 to 370 mm year−1 (about 17% of the total rainfall). Despite its intrinsic limitations, the SR method allowed robust recharge estimation with ability to cope with spatial and temporal variations, as well, especially in areas lacking hydrological monitoring programs. The SR method provides valuable information for water management policymakers and stakeholders to minimize impacts related to climatic variations and inappropriate land use on recharge processes.

Application of MIKE SHE software for estimation of groundwater recharge in Ogun and Oshun basins, southwestern Nigeria

Application of MIKE SHE software for estimation of groundwater recharge in Ogun and Oshun basins, southwestern Nigeria

Testing Evapotranspiration Estimates Based on MODIS Satellite Data in the Assessment of the Groundwater Recharge of Karst Aquifers in Southern Italy

In many Italian regions, and particularly in southern Italy, karst aquifers are the main sources of drinking water and play a crucial role in the socio-economic development of the territory. Hence, estimating the groundwater recharge of these aquifers is a fundamental task for the proper management of water resources, while also considering the impacts of climate changes. In the southern Apennines, the assessment of hydrological parameters that is needed for the estimation of groundwater recharge is a challenging issue, especially for the spatial and temporal inhomogeneity of networks of rain and air temperature stations, as well as the variable geomorphological features and land use across mountainous karst areas. In such a framework, the integration of terrestrial and remotely sensed data is a promising approach to limit these uncertainties. In this research, estimations of actual evapotranspiration and groundwater recharge using remotely sensed data gathered by the Moderate Resolution Imaging Spectrometer (MODIS) satellite in the period 2000–2014 are shown for karst aquifers of the southern Apennines. To assess the uncertainties affecting conventional methods based on empirical formulas, the values estimated by the MODIS dataset were compared with those calculated by Coutagne, Turc, and Thornthwaite classical empirical formulas, which were based on the recordings of meteorological stations. The annual rainfall time series of 266 rain gauges and 150 air temperature stations, recorded using meteorological networks managed by public agencies in the period 2000–2014, were considered for reconstructing the regional distributed models of actual evapotranspiration (AET) and groundwater recharge. Considering the MODIS AET, the mean annual groundwater recharge for karst aquifers was estimated to be about 448 mm·year−1. In contrast, using the Turc, Coutagne, and Thornthwaite methods, it was estimated as being 494, 533, and 437 mm·year−1, respectively. The obtained results open a new methodological perspective for the assessment of the groundwater recharge of karst aquifers at the regional and mean annual scales, allowing for limiting uncertainties and taking into account a spatial resolution greater than that of the existing meteorological networks. Among the most relevant results obtained via the comparison of classical approaches used for estimating evapotranspiration is the good matching of the actual evapotranspiration estimated using MODIS data with the potential evapotranspiration estimated using the Thornthwaite formula. This result was considered linked to the availability of soil moisture for the evapotranspiration demand due to the relevant precipitation in the area, the general occurrence of soils covering karst aquifers, and the dense vegetation.

Impacts of climate change on Moroccan’s groundwater resources: State of art and development prospects

The scientific knowledge of processes related to climate change impact on groundwater resources remains insufficient both nationally and internationally. This is due particularly to: the inadequacy of databases both quantitatively and qualitatively; Insufficient accuracy of predictions by climate models, especially rainfall and their sensitivity to the choice of climate scenarios; Insufficient accuracy of methods for estimating groundwater recharge; the difficulty of modelling surface water/groundwater interaction over large areas.The assessment of climate change impacts on groundwater resources requires reliable predictions of climate variables; a good estimation of groundwater recharge and its spatial and temporal variability; and the master of hydrodynamic response of the aquifer to different climate change scenarios.Several research studies have shown that climate change has accentuated negative repercussions on groundwater resources in Morocco. These studies were using different approaches: experimental, numerical and statistical modelling. Many aquifer problems were investigated regarding: saline intrusion; water resources quality; recharge, shortage of water reserves. This research works has rarely treating the different process aspects involved with integrated approach.Therefore, this paper focuses on the analysis of the effects of climate change on groundwater resources using a global and systemic approach that would take into account the multidisciplinary nature of the process: Climatic, hydrological and hydro-geological.

Estimation of potential groundwater recharge by a drywell in sandy clay soil

ABSTRACT We estimated the potential groundwater recharge (Rpot) of a drywell that receives, temporarily stores, and infiltrates direct surface runoff from a contribution area (180.5 m2) comprising a roof and a cemented floor. The Rpot for traditional rainwater management and for similar contribution area but covered with grass was also estimated for comparison. Our methodology involved the use of water budget equation, monitoring of rainfall and soil water content up to 1.92 m depth, estimation of drywell overflow using the modified Puls model, and determination of actual evapotranspiration using water stress coefficient in 2017 and 2018. Results revealed that the Rpot for drywell was 83.3% of the precipitated volume, 2.22 times higher than that of the grass-covered area (37.6%) given the increased area for evapotranspiration in the latter. In turn, the traditional urban drainage system did not demonstrate potential of groundwater recharge. Therefore, the drywell contributes significantly to groundwater recharge apart from serving as local flood control.

Estimation of Groundwater Recharge in Semarang City, Indonesia

In regional groundwater management, it is necessary to find out the water balance between the supply and demand of groundwater. One of the most important in analyzing the water balance of groundwater is groundwater recharge. Semarang city that has a groundwater management problem needs to know the groundwater recharge to analyze the groundwater balance. On the other hand, it is difficult to measure groundwater recharge accurately, consequently, the groundwater recharge should be estimated. There are several methods to estimate groundwater recharge. To verify the groundwater recharge estimation, more than one method of groundwater recharge estimation should be used. In this paper, the determination of groundwater recharge is using the Chaturvedi formula and Krishna Rao formula based on the amount of rainfall, and well level data method that based on the difference in water level. Based on the final results, the well level data method seems the best fit in estimating the groundwater recharge.

Evaluation of Groundwater Recharge based on Climate Change: A Case Study at Baung’s Watershed, Kota Bharu, Kelantan

The soil water assessment tool (SWAT) is a continuous and distributed hydrologic model created to simulate the effect of land management practices on water in the watershed. Understanding relationship of water extraction of groundwater can lead to better watershed management. The main problem in this study is the complexity of recharge processes and limited observations in groundwater recharge in Malaysia makes it difficult to quantify. This study was done at Baung’s watershed (BW) which can be considered as an ungauged watershed. The estimation of groundwater recharge in BW was done using SWAT. However, BW cannot be calibrated due to lack of streams station availability but the uncalibrated SWAT able to provide satisfactory predictions on hydrologic budget. A framework for SWAT input data including hydrography, terrain, land-use, soil, and weather for BW was then focused in order to achieve the model simulation for ungauged basins. The results emphasize the importance and prospects of using accurate spatial input data for the physically based SWAT model. Normal condition, extreme-low precipitation and future in land-use development represented as scenarios 1, 2, and 3 were evaluated in this study. These conditions give different groundwater recharge rate as different scenarios give different impact to groundwater. Model was found to produce a reliable estimation of groundwater recharge of 405 mm/year (14.6%), 194.12 mm/year (11.1%), and 214.23 mm/year (7.7%) for scenarios 1, 2, and 3, respectively. In conclusion, it suggested that groundwater recharge should not be assumed always 6% of annual rainfall in Malaysia as the factors influencing groundwater recharge need to be took into consideration in assisting groundwater exploration and management.

Estimation of Ground Water Recharge for Irrigation Water Budget Planning in Kanzenze Swamp

Groundwater is the dynamic local water source for agriculture, industry, wildlife and human development activity. Hence, in order to sustain long-term groundwater use, make intelligent groundwater allocation decisions and water budget planning, develop on-farm water management strategies, the estimation of the net groundwater recharge from agricultural areas like Kanzenze swamp is paramount important. The study findings therefore showed that Ground Water Recharge estimation for the study area ranges from 33.85mm to 52.96mm while the average mean of ground water recharge is about 45.06mm per year. The coefficient of ground water recharge is ranging from 3.41% to 5.27% while average mean recharge coefficient is 4.06% recharged to ground water level yearly. However, monthly basis planning have advantages for farmers’ water budgeting. It revealed that highest recharge coefficient is recorded in months of March, April and November representing 17.22% and 17% of the mean monthly rainfall while the lowest recharge coefficient is recorded during the period of June, July and February representing 16.17%, 15.73% and 16.71% of the average monthly rainfall. Thus, it is recommended that utmost farmers around the Kanzenze swamp should plan the irrigation activities and minimizes unnecessary water use consumption in such way that in June and July there is water enough water even taught there is shortage of rainfall. It meant that priori irrigation systems should be applied to obtain optimum moisture content and water table levels for effective crop production mainly horticultural crops in season C rather than season A and season B of cultivation in Rwanda.

Environmental tracers to evaluate groundwater residence times and water quality risk in shallow unconfined aquifers in sub Saharan Africa

In sub-Saharan Africa, shallow aquifer systems are relied on as the main safe and secure water resource available to rural communities. Information on the sustainability and vulnerability of groundwater abstraction is becoming increasingly important as groundwater development increases. As part of the UpGro Consortium Project- Hidden Crisis, 150 hand pumped boreholes (HPBs), ranging between 15 and 101 m depth were investigated to examine the resilience of aquifer systems in the Ethiopian Highlands, and the crystalline basement rocks of Uganda and Malawi. Environmental tracers (chlorofluorocarbons (CFCs), SF6, chloride and the stable isotopes of water), water quality indicators (nitrate and E. coli), and groundwater-level time series data were used to estimate groundwater residence time and recharge at a regional scale (100–10,000 km2) and investigate the risks to water quality and water supply over different timeframes, and geological and climatic environments. Average estimated recharge rates using three different techniques (CFCs, chloride mass balance, water table fluctuation method) were between 30 and 330, 27–110 and 30–170 mm y−1, for sites in Ethiopia, Uganda and Malawi, respectively. These estimates of recharge suggests abstraction from dispersed low-yielding HPBs is sustainable. Comparison of stable isotopes in rainfall and groundwater indicates that there is little evaporation prior to recharge, and recharge events are biased to months with greater rainfall and more intense rainfall events There was a weak correlation between nitrate and CFCs within all three countries, and no correlation between E. coli and CFCs within Ethiopia or Malawi. The presence of E. coli at a large proportion of the sites (Ethiopia = 38%, Uganda = 65% and Malawi = 47%) suggests rapid transit of contaminated surface water into the borehole and its presence in groundwater that has CFC-12 concentrations less than 75 pg kg−1 indicates mixing of very young water with water >40 years old. The rapid transit pathways are most likely associated with damaged HPB headworks and poor construction. In several monitored HPBs, daily drawdown due to pumping, drew the groundwater levels close to the base of the HPB, indicating that these HPBs were located in parts of the aquifer with low permeability, or were poorly designed, offering limited capacity for increased demand. Improved HPB siting and construction, coupled with groundwater level monitoring are required to capitalise on the more resilient groundwater within the shallow aquifers and safeguard adequate and good quality water supply for rural communities.