Simultaneous treatment of synthetic raw water containing natural organic matter (6 mg L−1) and clayey turbidity (0–20 NTU) was carried out with PACl on continuous upflow type pilot-scale models of pulsating floc blanket clarifier (PFBC) and conventional clariflocculator (CC) each designed for a capacity to treat about 8,000 liters per day, to understand mechanistic differences in their functioning. Fluidized bed of pre-flocculated particles prompted contact flocculation and enmeshment which lowered the residual turbidity for PFBC (0.07 ± 0.09 NTU) compared to CC (2.48 ± 1.71 NTU). Fine particles suspended in water clarified from PFBC and CC were hetero-disperse with Zavg as 2,341 nm and 5,693 nm respectively. On average, total residual aluminum was found to be 147 ± 33 ppb and 141 ± 51 ppb, while dissolved residual aluminum was found to be 31 ppb and 59 ppb for PFBC and CC respectively. Average total organic carbon reduction by PFBC and CC was 70.4% and 67.7% respectively. Size, structure and fractal dimensions of flocs were studied and average settling velocity of PFBC flocs was calculated to be 37% higher than CC flocs. Distinctness in characteristics of sludge formed in the two reactors has been highlighted by means of SEM micrographs and FT-IR spectra.