White-rot fungi (WRF) and their ligninolytic enzymes have been investigated for the removal of a broad spectrum of trace organic contaminants (TrOCs) mostly from synthetic wastewater in lab-scale experiments. Only a few studies have reported the efficiency of such systems for the removal of TrOCs from real wastewater. Wastewater derived organic and inorganic compounds can inhibit: (i) WRF growth and their enzyme production capacity; (ii) enzymatic activity of ligninolytic enzymes; and (iii) catalytic efficiency of both WRF and enzymes. It is observed that essential metals such as Cu, Mn and Co at trace concertation (up to 1 mM) can improve the growth of WRF species, whereas non-essential metal such as Pb, Cd and Hg at 1 mM concentration can inhibit WRF growth and their enzyme production. In the case of purified enzymes, most of the tested metals at 1–5 mM concentration do not significantly inhibit the activity of laccases. Organic interfering compounds such as oxalic acid and ethylenediaminetetraacetic acid (EDTA) at 1 mM concentration are potent inhibitors of WRF and their extracellular enzymes. However, inhibitory effects induced by interfering compounds are strongly influenced by the type of WRF species as well as experimental conditions (e.g., incubation time and TrOC type). In this review, mechanisms and factors governing the interactions of interfering compounds with WRF and their ligninolytic enzymes are reviewed and elucidated. In addition, the performance of WRF and their ligninolytic enzymes for the removal of TrOCs from synthetic and real wastewater is critically summarized.