Water quality monitoring is a major issue toward maintaining safety and security for many countries. Due to many contaminants present in surface water in the Republic of Moldova, groundwater monitoring has become an exclusive source of drinking and potable water for many cities. In this investigation, we determined chemical contaminants in groundwater bodies of the Prut River basin for groundwater classification. For this investigation, monitoring wells were sampled by several field trials. The results of the chemical analysis have been used for the preliminary identification, characterization, and classification of groundwater bodies. The chemical content of water shows the current status of groundwater bodies under investigation, thus validating the study on the importance of groundwater monitoring. We examined several heavy metals in the groundwater from a national monitoring network. One hotspot (contaminated region) is the old Chismichioi pesticide deposit, which was studied for the assessment of actual status of the surrounding territory. It is also one of the largest deposits of toxic substances in the Low Danube Euro region. The following spectrum of persistent organic pollutants was identified in the samples: DDE, DDD, DDT, a-HCH, b-HCH, and g-HCH. Several other toxic organic substances were also studied at this site, including PAHs, triazine pesticides, and some other heavy metals. The general conclusion about the situation around the Chismichioi deposit is that the level of pollution from the time of the origination (in 1979) has not changed, in general. The zones with high pollution levels should be eliminated and recommendations have been made for the mitigation of the negative impacts to the environmental and water resources in this area of Moldova. At the conclusion of this extensive investigation, similar studies are planned for other locations and surface water sources. This will provide a valuable tool for the Republic of Moldova and may be extended to other regions as well.