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Quantitative chemical analyses of 428 organic contaminants (OCs) confirmed the presence of 313 OCs in the sediment extracts from river Sava, Croatia. Pharmaceuticals were present in higher concentration than pesticides thus confirming their increasing threat to freshwater ecosystems. Toxicity evaluation of the sediment extracts from four locations (Jesenice, Rugvica, Galdovo and Lukavec) using zebrafish embryotoxicity test (ZET) accompanied with semi-quantitative histopathological analyses exhibited good correlation with cumulative number and concentrations of OCs at investigated sites (10,048.6, 15,222.8, 1,247.6, and 9,130.5 ng/g respectively) and proved its role as a good indicator of toxic potential of complex contaminant mixtures. Toxicity prediction of sediment extracts and sediment was assessed using Toxic unit (TU) approach and PBT (persistence, bioaccumulation and toxicity) ranking. Also, prior-knowledge informed chemical-gene interaction models were generated and graph mining approaches used to identify OCs and genes most likely to be influential in these mixtures. Predicted toxicity of sediment extracts (TUext) for sampled locations was similar to the results obtained by ZET and associated histopathology resulting in Rugvica sediment as being the most toxic, followed by Jesenice, Lukavec and Galdovo. Sediment TU (TUsed) favoured OCs with low octanol-water partition coefficient like herbicide glyphosate and antibiotics ciprofloxacin and sulfamethazine thus indicating locations containing higher concentrations of these OCs (Galdovo and Rugvica) as most toxic. Results suggest that comprehensive in silico sediment toxicity predictions advocate providing equal attention to organic contaminants with either very low or very high log Kow