Wastewater treatment is a critical and necessary task every human settlement is obligated to address. If not, the consequences might be catastrophic, not just for humans but for the ecosystems as well, pushing research into finding new ways to improve wastewater treatment processes to make them safer and more efficient. Hence, there is a need to address matters, such as reliability and maintainability of Wastewater Treatment Plants (WWTP), when analyzing the availability and operational conditions. These should be addressed by analyzing the plant operational effectiveness impact (P-OEI), and in this article specifically, a WWTP study case to identify design flaws or improvement opportunities. A vital aspect of a complex system is to determine the contribution to resilience, reliability, and availability of every element embedded in the system. This is performed by adapting and applying the P-OEI methodology and real data of a WWTP located in Chile. This methodology breaks down the system into several levels of disaggregation similar to RBD methodology, analyzing the upstream for availability and the downstream for the P-OEI analysis from the system itself to the individual elements within subsystems. The potential impact on the overall system’s lack of efficiency is also quantified by an Expected Operational Impact (EOI) index, which is also calculated by the methodology. The P-OEI and EOI analyses performed in this study are powerful tools to assess the design and performance of complex systems and WWTP in particular.