In recent years, there has been a surge in interest concerning emerging contaminants, also known as contaminants of emerging concern (CECs), due to their presence in environmental matrices. Despite lacking regulation, these chemicals pose potential health and environmental safety risks. Disodium EDTA, a widely utilized chelating agent, has raised concerns regarding its environmental impact. The present work aimed to verify the presence of Disodium EDTA at the exit of eight wastewater treatment plants discharging into some losing streams flowing within a large alluvial aquifer. Conducted in the Province of Parma (Northern Italy), the research employs a multidisciplinary approach, incorporating geological, hydrogeological, chemical, and microbial community analyses. Following a territorial analysis to assess industries in the region, through the use of ATECO codes (a classification system for economic activities), the study investigated the concentration of Disodium EDTA in effluents from eight diverse wastewater treatment plants, noting that all discharges originate from an activated sludge treatment plant, released into surface water courses feeding the alluvial aquifer. Results revealed detectable levels of Disodium EDTA in all samples, indicating its persistence post-treatment. Concentrations ranged from 80 to 980 µg/L, highlighting the need for further research on its environmental fate and potential mitigation strategies. Additionally, the microbial communities naturally occurring in shallow groundwater were analyzed from a hydrogeological perspective. The widespread presence of a bacterial community predominantly composed of aerobic bacteria further confirmed that the studied aquifer is diffusely unconfined or semi-confined and/or diffusely fed by surface water sources. Furthermore, the presence of fecal bacteria served as a marker of diffuse leakage from sewage networks, which contain pre-treated wastewater. Although concentrations of Disodium EDTA above the instrumental quantification limit have not been found in groundwater to date, this research highlights the significant vulnerability of aquifers to Disodium EDTA. It reveals the critical link between surface waters, which receive treated wastewaters impacted by Disodium EDTA, and groundwater, emphasizing how this connection can expose aquifers to potential contamination. At this stage of the research, dilution of wastewaters in surface- and groundwater, as well as hydrodynamic dispersion within the alluvial aquifer, seem to be the main factors influencing the decrease in Disodium EDTA concentration in the subsurface below the actual quantification limit. Consequently, there is a pressing need to enhance methodologies to lower the instrumental quantification limit within aqueous matrices. In a broader context, urgent measures are needed to address the risk of diffuse transport of CECs contaminants like Disodium EDTA and safeguard the integrity of surface and groundwater resources, which are essential for sustaining ecosystems and human health.