During the process of pollutants infiltrating and recharging groundwater from surface water, the migration process and flux of pollutants are notably influenced by the local hydrodynamic characteristics and biogeochemical processes within the hyporheic zone [18; 19]. Differences in flow pathways, velocities, residence times, and the exchange between surface water and groundwater control the reactive transport of, and affect the flux in, pollutants. In the process of pollutants from the vadose soil environment entering the groundwater system, their adsorption, migration, and transformation within the geological media are complex and take forms such as surface runoff, leaching, erosion, desorption, and dissolution [19; 20; 21]. This complexity encompasses factors including the soil lithology, porosity, moisture content, pollutant type and concentration, oxidation-reduction potential (ORP), pH, organic matter, cation exchange capacity, microbial communities, etc. [22; 23]. It is worth noting that certain elements (e.g., phosphorus, iron, fluoride, arsenic, iodine, uranium, and molybdenum,) are naturally abundant in the form of minerals/rocks in soils and groundwater sediments [3; 24; 25; 26]. Although elevated levels of these inorganic constituents are often attributed to geogenic processes such as weathering, leaching, and water-rock interactions, anthropogenic activities can be expected to introduce and further intensify the contaminations [27; 28; 29]. These contaminants are primarily derived from domestic, agricultural, and industrial sources, including the application of fertilizers and pesticides in agricultural production, irrigation with sewage (or reclaimed water), leakage from domestic sewage networks and landfill site wastewater, waste residues generated during mining, or oil and gas field exploitation. [1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16; 17; 18; 19; 20]. For instance, fluctuations in groundwater levels caused by either natural or anthropogenic processes accelerate the leaching of organic matter, nitrogen, and heavy metals from the soil into shallow groundwater [30] and affect the aquifer redox cycling and microbial activity [31]. Intensive groundwater pumping can draw recently recharged contaminated modern groundwater into deeper aquifer systems [32]. Petroleum and natural gas exploitation causes petroleum hydrocarbon and salinity contamination in the vadose zone [33] and shallow groundwater [34]. Furthermore, the role of metals (e.g., Hg, Zn, Cu, and Cd) in co-selecting antibiotic resistance might be important in the spread of antibiotic resistance genes [20]. The speciation of contaminants adds another layer of complexity to the soil-groundwater environment. As pollutants interact with the soil matrix and microbial communities, they undergo chemical transformations, altering their properties and toxicity. Contaminants can undergo different chemical transformations, resulting in various species with different properties and toxicities. Metals can exist in different oxidation states, and organic contaminants can undergo degradation or transformation into metabolites and greenhouse gases. The speciation of contaminants affects their mobility, bioavailability, and toxicity, and an understanding of these forms is crucial to accurately assessing their environmental impact and risk. For instance, arsenic (As) primarily exists as As(V) and can transform into more mobile As(III) under reducing conditions, affecting the groundwater quality [35]. Chromium (Cr) exists as both the Cr(VI) and Cr(III) forms, with Cr(VI) becoming soluble and migrating into groundwater under oxidizing conditions [36]. Uranium (U) in soil and sediments is typically found as less mobile U(IV) compounds, while, in groundwater, it exists as more mobile uranyl U(VI) and UO\({}_{2}\)\({}^{2+}\) complexes, which are strongly influenced by various groundwater physicochemical factors [37]. Redox conditions and natural organic matter play key roles in these transformations [24; 29; 38; 39].