Access to safe, reliable drinking water is a major problem in Sub-Saharan Africa, particularly in rural and peri-urban regions [1]. A large population relies on untreated water sources from rivers, wells and boreholes, which are susceptible to contamination by organic matter, animal waste and surface pollutants. Waterborne diseases like cholera and typhoid fever, remain prevalent in some of these regions [2][3]. This problem is worsened by aging infrastructure, leaking pipes, poor maintenance, delayed upgrades and mismanaged public funds, which disproportionately affect rural areas and increase reliance on groundwater [4].

Water drilling predates millennia and continues to provide a reliable, independent and inexpensive water source [5]. Although combination of natural and anthropogenic factors make up the quality of groundwater as well as natural processes like rock weathering, mineral dissolution, cation exchange and redox reactions. Additionally, soil properties, including mineral composition, permeability and organic matter content control the mobility of ions and trace metals [6][7]. Anthropogenic activities such as agriculture, wastewater discharge, pit latrines, septic tanks and livestock farming introduce contaminants that can percolate into aquifers and compromise groundwater quality [8][9].

Previous studies in Limpopo Province reported wide variation in physicochemical parameters like pH, salinity, electrical conductivity, total dissolved and microbial loads between boreholes, influenced by local geology, climate and land-use [10]. However, groundwater quality in many subregions, including Zebediela, remains poorly characterized, so communities often consume groundwater without knowing its safety or compliance with WHO and SANS drinking water [11]. The Zebediela subregion relies extensively on groundwater for domestic, agricultural and recreational use. The combination of semi-arid climatic conditions, diverse soil types, sedimentary geology and intensive agricultural activities creates complex hydrochemical interactions that influence groundwater quality [12][13]. This study aimed to evaluate the hydrochemical composition, microbial contamination and heavy metal concentrations in borehole water from Zebediela subregion.

Water quality assessment is imperative for public health and sustainable freshwater resources. Regular monitoring improves understanding of hydrochemical systems and supports resource management practices. This study investigated the chemical quality, heavy metal levels and microbial status of underground water collected from Zebediela subregion. The samples showed soft to moderately hard water (Figure 1(a)), like that reported by [17] in Ga-Matlala village in Limpopo, attributed to dissolution of calcium-magnesium carbonates and bicarbonates. Although not acutely toxic at this level, increased detergent and soap use can indirectly damage household infrastructure from chemical accumulation [18].

Sulphate evinced a greater spatial variation than hardness, most likely due to the dissolution of evaporite minerals or to lithological control rather than surface contamination. This contrasts with surface contamination, which typically manifests in primary aesthetic effects. Comparable sulphate enrichment has been reported in borehole water systems in the Vhembe district of Limpopo Province [19]. Adverse health effects related to exposure to sulphate at such low concentrations are generally confined to taste alteration and laxation effects in non-acclimated consumers [20]. Cumulative exposure to undesirable concentrations (above the recommended 1.5 mg·L⁻ by WHO) of F⁻ is concerning. Exposure to excessive F⁻ can lead to disturbances of bone homeostasis and enamel development [21]. The most likely cause of F⁻ enrichment is the geochemical weathering of fluoride-bearing minerals. This is further enhanced by low rainfall, high evaporation rates and elevated pH in Zebediela. The concurrent enrichment of F⁻ alongside elevated SO 4 2 − concentrations and increased water hardness observed in several boreholes in Zebediela subregion may suggest prolonged water-rock interactions [22].

Elevated NO 3 − concentrations in regions characterized by intensive cropping are indicative of fertilizer-derived nitrate inputs. Accordingly, the occurrence of increased nitrate levels in Zebediela is plausible, given its designation as an area of high agricultural productivity. Similarly, comparable NO 3 − distributions in agriculturally impacted groundwater from Albert, Canada [23]. Chronic exposure to NO 3 − is associated with Methaemoglobinemia in infants and the in vivo conversion of NO 3 − to N-nitroso compounds has been associated with multiple systemic health effects, particularly through their mutagenic and carcinogenic potential [24]. Additionally, the presence of both nitrate and microbial contamination in some of the boreholes may lead to a greater incidence of gastrointestinal infections, due to microorganisms ability to facilitate the conversion of nitrate into nitrite [25] (Figure 2).

Moderate COD and BOD levels observed in Zebediela subregion groundwater (Figure 1(a)) suggested the presence of organic contaminants, potentially associated with surface activities and borehole exhibiting limited attenuation due to short subsurface travel. Although the COD and BOD measured in this study did not indicate severe organic pollution, they are indicative of sustained input of organic matter into the groundwater system [26]. Under such environmental conditions, the co-existence of a small amount of readily-biodegradable organic matter provides sufficient substrate to maintain viable population levels of heterotrophic bacteria and the potential proliferation of pathogenic organisms. This risk is particularly pronounced in rural borehole systems, where disinfection practices are either sporadic [27] or do not exist.

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Figure 2. (a) Flow diagram showing the distribution and development of specific microorganisms in positive samples. Numbers indicate the count of samples positive for each microbial group or combination. (b) Bar chart showing the percentage occurrence of key microbial indicators and pathogens.

Heavy metals constitute one of the most widespread groups of groundwater contaminants, with their presence reflecting a combination of geogenic contributions and anthropogenic inputs. In the Zebediela subregion, intensive citrus cultivation, extensive limestone mining and unregulated waste disposal practices represent potential sources of metal contamination. Over time, these activities have enhanced chemical loading in the subsurface environment and facilitated the infiltration of landfill derived leachates into local aquifers [28]. The hydrogeochemical quality system of the groundwater system (Table 2) was influenced by the metal speciation, transport and bioavailability, as suggested by the multivariate statistical analyses (Figure 3). Increased bicarbonate and sulphate concentrations enhance the mobility of metals such as lead and cadmium through the formation of carbonate and sulphato-complexes, respectively, while increased chloride levels promote metal solubility via the formation of thermodynamically stable chloro-complexes [29].

Figure 3. Present images depicting selected results from microbial detection in borehole water and colony development after incubation.

These associations are consistent with the observed correlations between major ions and trace metals and the PCA loadings (Figure 4), which suggest shared geochemical drivers and potential common sources. In addition, variations in pH also play a fundamental role in regulating metal behaviour, as acidic conditions can induce the desorption of metals from the solids phase of the aquifer and destabilize metal carbonate complexes, resulting in increased dissolved metals [30].

Elevated levels of iron and manganese have been recorded in a number of boreholes over an extended period of time (Figure 1(b)), which demonstrate the occurrence of redox conditions within different sections of the aquifer system. The reductive dissolution of iron and manganese oxides under these redox conditions results in the release of dissolved ferrous ion (F²⁺) and dissolved manganous ion (Mn²⁺) into groundwater while also causing the mobilization of trace metals adsorbed to aquifer solids including Pb, Cd and As [31]. Elevated Mg and Fe are associated with other trace metals which suggests that redox-driven mobilization of trace metals is likely occurring at the sites of contamination, as opposed to independent or separate contamination events. Arsenic is one example where its mobility is directly related to the dissolution of iron oxyhydroxides [32].

Figure 4. Correlation matrix of organic water quality parameters. The heatmap shows Pearson correlation coefficient (r) from −1 (dark blue, strong negative) to +1 (dark red, strong positive), with significant relationships (r ≥ 0.5) highlighted.

The detection of faecal indicator bacteria such as Escherichia coli and enteric bacteria (Table 4) confirms faecal contamination of the groundwater system. Such contamination can probably be attributed to inadequately sited pit latrines, the concentration of shallow borehole and enhanced surface infiltration which make aquifers prone to microbial ingress [33]. Similar microbial contamination profiles of both total coliform and E. coli were detected in domestic borehole water from Vhembe District, Limpopo Province. The co-occurring patterns found in the microbiota (Figure 1(a), Figure 1(b)) imply shared contamination pathways rather than isolated events and a common source or transport mechanism consistent with network-based microbial ecology models [34]. When considered alongside elevated COD, BOD and nitrate levels, these indicate a sustained surface-derived contamination and limited natural attenuation within the aquifer system. These conditions are an important public health issue, as faecal contamination of drinking water is strongly associated with increased risks of waterborne disease, including gastroenteritis, dysentery, cholera and typhoid fever [35][36].

The results of the correlation analyses indicated a combination of weak, moderate and strong correlations among the major ions and physicochemical parameters in addition to indicating influence on the quality of groundwater by multiple controlling processes. The inverse association NO 3 − with SO 4 2 − (Table 2) also suggests that nitrate and sulphate enrichment may be occurring through processes other than the dissolution of carbonates (i.e., agricultural inputs or anthropogenic influences). These ions appear to be derived from either evaporative concentration of groundwater or anthropogenic contamination because of the presence of Cl⁻ and SO 4 2 − (r = 0.47). moderate correlations were observed for Pb with both Fe (r = 0.40) and COD (r = 0.24); these correlations could indicate the occurrence of adsorption/desorption processes or co-mobility of Pb and Fe under similar geochemical conditions. Pb exhibits moderate correlations with both Fe r = 0.40 and COD r = 0.24, which could indicate the occurrence of adsorption/desorption processes or co-mobility of Pb and Fe under similar geochemical conditions.

Figure 5. The plot shows variable loadings (vectors) for the first two principal components (PC1 and PC2), which explain 32.7% of the dataset variance. The length and direction of each vector indicate the strength and correlation of each parameter with the components.

As shown in Figure 5, PCA indicates that PC1 and PC2 explained 16.6% and 16.1% of the total variance, respectively, accounting for a cumulative variance of 32.7%. Although this cumulative variance is relatively low, such variance distribution is typical of complex hydrogeochemical systems influenced by multiple natural and anthropogenic processes, where no single factor dominates groundwater chemistry [37][38]. PC1 was primarily loaded with organic pollution and metal-related parameters including Pb, BOD, COD and Fe suggesting a possible pollution gradient exists due to local contamination sources, like agricultural runoff or domestic waste disposal. Conversely, variables that loaded negatively on PC1, such as hardness and As, suggest that these variables are largely controlled by geogenic processes (i.e., mineral weathering) rather than anthropogenic activities. PC2 showed strong loading for nutrients and major ions ( NO 3 − , SO 4 2 − , Cl⁻ and Mg), suggesting geochemical and fertilizer applications and/or evaporative concentration effects. Additional variance was distributed across higher-order components, indicating the contribution of localized or site-specific hydrogeochemical controls.

In the present study, the quality of borehole water composition from Zebediela subregion, was utilized for the presence of major ions, trace metals and biological content compared to the drinking water standards. It is concluded that none of the major ions exceeded the permissible limits by WHO except for heavy metals Cd and As which were found fairly above for domestic use. Biological analysis revealed faecal indicator in 80% of the samples, demonstrating the ability of microorganism growth in groundwater due to external influence. Although groundwater in Zebediela subregion is essential for domestic, agricultural, and recreational use, microbial contamination and localized exceedances of some parameters mean it is not consistently safe for direct consumption. Regular monitoring, improved sanitation, borehole protection, and community education on safe water handling are needed to safeguard public health. The findings provide a critical baseline for sustainable groundwater quality management in Zebediela subregion.