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Cyanobacteria produce complex mixtures of secondary metabolites (cyano-metabolites), some of which are toxic and pose a growing concern for water utilities. While physical treatments such as filtration can efficiently remove cells, their lysis can release dissolved cyano-metabolites. This study investigated the efficiency of laboratory-scale sand filtration to abate 19 cyano-metabolites representing various structural classes. Furthermore, abatement of cyanometabolites in a full-scale sand filtration is presented. Most cyano-metabolites showed abatement similar to or higher than the biodegradable benchmark micropollutants atenolol, paracetamol, and valsartan. Among cyano-metabolites, anabaenopeptins and cyanopeptolins had the highest abatement, while cyclamides and microcystin-LR had the lowest abatement. Abiotic controls and formation trends of 10 identified biotransformation products demonstrated that biodegradation played a major role in their removal. Laboratory-scale sand filters showed a sharp increase in biodegradation efficiency within days due to their adaptation to cyano-metabolites. Increasing the contact time and temperature both enhanced the abatement of most compounds, which could be kinetically modeled. High cyano-metabolite concentrations suppressed their own relative abatement, possibly due to metabolic enzyme inhibition or saturation. These findings suggest that sand filtration can serve as a dual-barrier against cyano-metabolites, including particle removal and biodegradation. However, biodegradation will be affected by the temperature and cyano-metabolite intake dynamics.