Pulp and paper mills generate a plethora of pollutants depending upon the type of pulping process. Efforts to mitigate the environmental impact of such effluents have been made by developing more effective biological treatment systems in terms of biochemical oxygen demand, chemical oxygen demand, colour and lignin content. This study is the first that reports an evaluation of the effects of a tertiary treatment by fungi (Pleurotus sajor caju, Trametes versicolor and Phanerochaete chrysosporium and Rhizopus oryzae) on individual organic compounds of a Eucalyptus globulus bleached kraft pulp and paper mill final effluent after secondary treatment (final effluent). The tertiary treatment with P. sajor caju, T. versicolor and P. chrysosporium and R. oryzae was performed in batch reactors, which were inoculated with separate fungi species and monitored throughout the incubation period. Samples from effluent after secondary and after tertiary treatment with fungi were analysed for both absorbance and organic compounds. The samples were extracted for organic compounds using solid-phase extraction (SPE) and analysed by gas chromatography-mass spectrometry (GC/MS). The efficiencies of the SPE procedure was evaluated by recovery tests. A total of 38 compounds (carboxylic acids, fatty alcohols, phenolic compounds and sterols) were identified and quantified in the E. globulus bleached kraft pulp mill final effluent after secondary treatment. Recoveries from the extraction procedure were between 98.2% and 99.9%. The four fungi species showed an adequate capacity to remove organic compounds and colour. Tertiary treatment with R. oryzae was able to remove 99% of organic compounds and to reduce absorbance on 47% (270 nm) and 74% (465 nm). P. sajor caju, T. versicolor and P. chrysosporium were able to remove 97%, 92% and 99% of organic compounds, respectively, and reduce 18% (270 nm) to 77% (465 nm), 39% (270 nm) to 58% (465 nm) and 31% (270 nm) to 10% (465 nm) of absorbance, respectively. The wide variety of organic compounds found in the final effluent must be due to the degradation of E. globulus wood in pulp and paper mill. The concentrations of organic compounds in the final effluent of E. globulus bleached kraft pulp mill were in residual levels maybe due to the secondary treatment. The recovery tests showed the effectiveness of the extraction procedure, and no losses of analyte were suspected in the analytical determinations. Lignin derivatives such as vanilic acid, syringic acid, guaiacol, syringol and phloroglucinol were totally removed by R. oryzae, but the 47% absorbance reduction obtained at 270 nm suggests that these species were not able to complete degradation of lignin macromolecular compounds. The organic compounds (carboxylic acids, fatty alcohols, phenolic compounds and sterols) were removed more efficiently by tertiary treatment with R. oryzae or P. chrysosporium, followed by P. sajor caju and T. versicolor. Regarding the removal of both colour and organic compounds, the tertiary treatment with R. oryzae was the most efficient. In order to reduce the deleterious impacts of paper mill effluents, efforts have been made to develop more effective advanced tertiary treatments. This study may serve as a basis of characterisation, in terms of organic compounds of E. globulus bleached kraft pulp mill final effluent after secondary treatment and as an effort to understand the effects of tertiary treatments with fungi on low concentrations of organic compounds from biological secondary treatment.