Flocculation using modified clays is a technique widely applied in the management of harmful algal blooms (HABs). Polyaluminum chloride (PAC) modified clay is an efficient flocculating agent in HAB control; however its effectiveness in black bloom management is still largely unknown. In the present study, PAC-modified clay was used to flocculate a black bloom under simulated flows. The deposition and resuspension of the black matter/clay flocs and the impact of the spreading of quartz sand to the flocs were quantitatively studied. The results showed that a dosage of 1.8 g/L PAC-modified clay (0.8 g/L PAC and 1 g/L diatomite) could reduce turbidity by more than 90% in 1 h. The resuspension of flocs could be generated by a threshold bed shear stress of 0.045 N/m2. The addition of quartz sand inhibited the resuspension of flocs. We suggest that quartz sand can be used to effectively inhibit floc resuspension caused by waves and flow currents as the subsequent treatment of black bloom flocculation in Lake Taihu.