Trace organic compounds are important in environmental analysis because they impact water quality and introduce potential (eco)toxicological effects. Current analytical methods mostly rely on gas chromatography (GC) or reversed-phase liquid chromatography (RPLC) coupled with (tandem) mass spectrometry. However, neither method can easily separate very polar molecules. This study presents two chromatographic separation strategies, a serial RPLC–hydrophilic interaction liquid chromatography (RPLC-HILIC) coupling and an analytical scale supercritical fluid chromatography (SFC) system, and validates their separation effectiveness as polarity-extended chromatographic methods for 274 environmentally relevant compounds. Compounds tested were grouped into three polarity classes, “very polar” {log D (pH 7) below −2.5}, “polar” {log D (pH 7) −2.5 to +2}, and “non-polar” {log D (pH 7) higher than +2}). Nearly all compounds could be retained in both systems with relative standard deviations of retention times (RT; n = 6) typically between 2 and 5%. Both techniques have considerable benefits when combined with accurate mass spectrometric detection. Molecules RT and accurate mass were recorded in a database for each set up. This information was used for compound screening measurements like “hidden-target screening” in complex environmental matrices (such as wastewater treatment plant effluents). Results of both techniques are complementary and useful for all types of molecules polarity. In this study, more than 80% of the compounds found in wastewater treatment plant effluent samples possessed a negative log D (pH 7) value. This result highlights the basic necessity to include “very polar” compounds in water monitoring techniques and protocols.