In recent decades, small domestic wastewater treatment plants have become popular in rural areas of the Slovak Republic. The reason for the expansion of decentralized wastewater management is that many rural areas have scattered settlements, and a centralized wastewater disposal system is economically, technically demanding, and inefficient. The disadvantage of using small domestic treatment plants in terms of environmental protection is that these facilities have yet to be significantly monitored. Due to improper operation and maintenance, they can have a long-term negative impact on the environment and jeopardize the quality of water resources. Currently, a new law amendment is being introduced in Slovakia to promote regular inspections of these facilities. The aim of this contribution is to summarize the knowledge in the field of decentralized wastewater treatment in rural areas, present the new legislative framework, and focus on the need to develop a methodology for addressing identified problematic sites and proposing measures to ensure the good condition of groundwater and surface water in the territory of the Slovak Republic.