Over the last decade, human activities in the industrial and agricultural sectors have significantly increased the concentration of persistent and harmful pollutants in aquatic ecosystems. The use of microorganisms is a green strategy for the bio-removal of certain contaminants. However, other pollutants in the same ecosystems can reduce their degrading activity and even affect their survival. Therefore, this study aimed to evaluate the efficiency of benzo(b)fluoranthene (BbF) and benzo(k)fluoranthene (BkF) removal by Selenastrum capricornutum in the presence of triazine herbicides, compounds mainly used in broadleaf weeds. The interest of this work focused on identifying in which of the microalgal components the degrading activity is best evidenced and affected. For this purpose, the use of solid-phase extraction (SPE) and matrix solid-phase dispersion (MSPD) extraction procedures and HPLC-UV analysis allowed the BbF and BkF trace quantification in biomass, liquid medium, and cell lysate separately from cultures exposed to these polycyclic aromatic hydrocarbons (PAHs) alone or with herbicides. The recovery percentages were between 78 and 94 %, good linearity (r2 ≈ 0.99), precision values measured as RSD < 15 %, and limits of detection (LOQs) at levels of ng mL−1 and ng mg−1 were obtained. The individual PAH amounts measured in the components of microalgae cultures show similar removal kinetics (removal percentages: 82–89 %). Likewise, the analysis demonstrated that the removal of PAHs is not affected in the presence of triazine herbicides (atrazine and cyanazine) and with similar removal percentages (79–86 %) compared to those cultures exposed to individual PAHs (74–83 %). These results support the possible real-world applications of PAH removal by extracts from S. capricornutum in aquatic environments contaminated with PAHs and near agriculture areas where triazine herbicides are used.