The efficiency of several lab scale treatments (aerobic, anaerobic and ozone or combination of these) was evaluated using two packaging board mill whitewaters. The effect of the different treatments on the elimination of the organic load, the chemical oxygen demand (COD) and the toxicity was tested as well as the relationship between these parameters. Biocides, phenolic compounds, surfactants, plasticiziers and wood extractives were identified in untreated and treated whitewaters by liquid chromatography coupled with mass spectrometry (LC-MS) or gas chromatography coupled with mass spectrometry (GC-MS). A strong dependency on the water type and treatment efficiency was observed, being the combination of anaerobic and aerobic treatments the best option to reduce the organic contaminants in these waters, although in some cases, the toxicity did not decrease. However, ozone as post-treatment permitted a further reduction of organic compounds, toxicity and COD.