The Environmental Impact Assessment (EIA) is a legal and administrative tool aimed to identify, predict, and interpret the impact of a project or activity on the environment and human health. The EIA also evaluates the accuracy of the predictions and audits the effectiveness of the established preventive measures. Regarding the sanitation sector, efficiency of wastewater treatments and sanitation networks determine the pollutant level of the discharged liquid effluents and the subsequent impact on the environment and human health. This problematic makes necessary to assess how proper the regulatory follow-ups of sanitation projects is. This paper evaluates the performance of the Chilean EIA System concerning to sanitation projects. Taking into account that the more restrictive Environmental Impact Study (EIS) and more permissive Environmental Impact Declaration (EID) are the ways for projects' entry to the EIA System in Chile, 5336 sanitation projects submitted to EIA between 1994 and 2019 were complied. A representative sample of 76 projects (15 entered as EIS and 61 as EID) was analyzed by using a principal coordinate analysis (PCoA) through 14 selected performance indicators. Observed weaknesses have led to propose improvement opportunities of the EIA focused on the follow-ups after the environmental license is obtained, such as creation of a simplified sanctioning procedure, decentralization of decision-making, deadline establishment in each stage, and unified direct link for each project. These proposals seek to improve the effectiveness of monitoring and possible sanctions to early identify impacts of sanitation projects on the environment and human health. This paper introduces a robust methodology for evaluation criteria focused on the follow-ups analysis, which can be used in other countries that consider respectful sanitation projects have direct social and environmental benefits leading to long-term indirect cultural and economic values.