Besides the physicochemical characteristics (e.g., size, structure, charge nature, etc.) of turbid particles, the filtration flow direction may affect their migration and adhesion behaviors inside the filtration unit. Unfortunately, there has been a lack of research regarding the combined effects of these above factors on filtered water quality and head loss development during filtration. In this study, different turbid particles were prepared by flocculating water samples containing kaolin and humic acid. Filtration experimental results of these flocculated waters revealed that downflow and upflow filtration modes had different durations of effective filtration under identical PAC-dosage cases, and upflow filtration led to faster increases in filtered water turbidity at the breakthrough stage compared to downflow filtration. During 180-min downflow filtration, the average size of residual turbid particles increased, but this did not occur in upflow filtration. Furthermore, differently from downflow filtration, upflow filtration had a more uniform distribution of head loss across all filter layers. The ease of backwashing differed between the two filtration modes, reflected by the different times required for reaching a relatively stable turbidity during 10-min backwashing. Lastly, based on SEM, FTIR and XPS analyses for characterizing the coagulated particle surface morphology, element composition, and functional groups, a series of conceptual models for particle removal by downflow and upflow filtrations were developed to clarify the influencing mechanisms of different turbid particles on filtration. It highlighted the advantages of upflow filtration, including improved distribution of flow resistance, better removal of larger-sized turbid particles, and enhanced pollutant-holding capacity of the filter media.