Over the last decades, as a consequence of wastewater discharges and other anthropogenic sources, severe nitrate (NO3−) pollution has developed in municipal environment causing global concern. Thus, eliminating the potential sources of pollution is one of the major challenges of the twenty-first century, whereby sanitation services are essential for ensuring public health and environmental protection. In the present study, long-term monitoring (2011–2022) of shallow groundwater NO3− contamination in municipal environment was carried following the construction of the sewerage network (2014) in the light of the pre-sewerage situation. Our primary aim was to assess the long-term effects of sewerage on nitrate NO3− levels in the shallow groundwater and evaluate the efficiency of these sanitation measures over time. Based on the results, significant pollution of the shallow groundwater in the municipality was identified. During the pre-sewer period, NO3− concentrations exceeded the 50 mg/L limit in the majority of monitoring wells significantly, upper quartile values ranged between 341 and 623 mg/L respectively. Using Nitrate Pollution Index (NPI) and interpolated NO3− pollution maps, marked spatial north–south differences were detected. In order to verify the presence of wastewater discharges in the monitoring wells, the isotopic ratio shifts (δ) for 18O and D(2H) were determined, confirming municipal wastewater effluent. Variations in NO3−/Cl− molar ratios suggest also contamination from anthropogenic sources, including septic tank effluent from households and the extensive use of manure. Data series of 7 years (2015–2022) after the investment indicate marked positive changes by the appearance of decreasing trends in NO3− values confirmed by Wilcoxon signed rank test and ANOVA. By comparing the pre- and post-sewerage conditions, the mean NO3− value decreased from 289.7 to 175.6 mg/L, with an increasing number of monitoring wells with concentrations below the limit. Our results emphasise the critical role of sanitation investments, while also indicating that the decontamination processes occur at a notably slow pace. Detailed, long-term monitoring is therefore essential to ensure accurate follow-up of the ongoing changes. The results can provide information for local citizens and authorities to improve groundwater management tools in the region.