(1) Background: Monitoring effluent in water treatment plants has a key role in identifying potential pollutants that might be released into the environment. A non-target analysis approach can be used for identifying unknown substances and source-specific multipollutant signatures. (2) Methods: Urban and industrial wastewater effluent were analyzed by HPLC-HRMS for non-target analysis. The anomalous infiltration of industrial wastewater into urban wastewater was investigated by analyzing the mass spectra data of "unknown common" compounds using principal component analysis (PCA) and the Self-Organizing Map (SOM) AI tool. The outcomes of the models were compared. (3) Results: The outlier detection was more straightforward in the SOM model than in the PCA one. The differences among the samples could not be completely perceived in the PCA model. Moreover, since PCA involves the calculation of new variables based on the original experimental ones, it is not possible to reconstruct a chromatogram that displays the recurring patterns in the urban WTP samples. This can be achieved using the SOM outcomes. (4) Conclusions: When comparing a large number of samples, the SOM AI tool is highly efficient in terms of calculation, visualization, and identifying outliers. Interpreting PCA visualization and outlier detection becomes challenging when dealing with a large sample size.