To remove organic contaminants from wastewater using cost-efficient and currently existing methods, our study investigated char-fortified filter beds for on-site sewage treatment facilities (OSSFs) in a long-term field setting. OSSFs are commonly used in rural and semi-urban areas worldwide to treat wastewater when municipal wastewater treatment is not economically feasible. First, we screened for organic contaminants with gas chromatography and liquid chromatography mass spectrometry-based targeted and untargeted analysis and then we developed quantitative structure-property relationship models to search for key molecular features responsible for the removal of organic contaminants. We identified 74 compounds (24 confirmed by reference standards) including plasticizers, UV stabilizers, fragrances, pesticides, surfactant and polymer impurities, pharmaceuticals and their metabolites, and many biogenic compounds. Sand filters that are used as a secondary step after the septic tank in OSSFs could remove hydrophobic contaminants. The addition of biochar significantly increased the removal of these and a few hydrophilic compounds (Wilcoxon signed-rank test, alpha = 0.05). Besides hydrophobicity-driven sorption, biodegradation was suggested to be the most important removal pathway in this long-term field application. However, further improvements are necessary to remove very hydrophilic contaminants as they were not removed with sand and biochar-fortified sand.