•Fungus was used as a template for the assembly of CNTs.•Fungal template enhanced the dispersity and stability of CNTs.•FH/CNTs exhibited high sorption capacity for U(VI) (187.26 mg/g), MV (43.99 mg/g) and CR (20.89 mg/g).•FH/CNTs possessed satisfactory regeneration performance and reusability.•FH/CNTs has a good selectivity on U(VI). In this paper, a biological assembly method was used to fix carbon nanotubes (CNTs) onto fungal hyphae (FH) to prepare sphere FH/CNTs composite as a versatile adsorbent for water pollution control. Physico-chemical characterization results showed that FH/CNTs composites had a wire stacking surface morphology, showed a typical diffraction peak of CNTs, was rich in functional groups, and was negatively charged under pH 3 to 10. Adsorptions of uranium (U(VI)), anionic (Congo red (CR)) and cationic (methyl violet (MV)) dyes under various conditions were investigated to elucidate their adsorption performances and mechanisms. Results showed that the composites could efficiently remove U(VI)), CR and MV from solutions. For example, the maximum adsorption amounts of FH/CNTs composites for U(VI), CR and MV reached 187.26, 43.99 and 20.89 mg/g, respectively. The adsorption process was fitted better by pseudo-second order model, while both of Langmuir and Freunlich models were well fitted to the adsorption isotherms for these pollutants. Moreover, the composites could be easily separated after adsorption and efficiently reused. Thus FH was an efficient platform for the assembly of CNTs, and the as-prepared FH/CNTs composites had the potential application in water pollution control.