In membrane-based water and wastewater treatment processes, understanding the interactive effect of various types of organic components on membrane fouling is crucial in order to identify effective fouling mitigation strategies. In this study, the effect of humic acid on alginate filtration was examined under both dead-end and crossflow constant flux microfiltration conditions using low viscosity and medium viscosity alginate as model foulants. The presence of humic acid (100 mg/L) appeared to accelerate alginate fouling under both dead-end and crossflow filtration conditions, following cake layer filtration mechanism (dead-end) and a combined intermittent pore blocking and cake layer filtration mechanism (crossflow) respectively. Under the crossflow filtration condition, the fouling mechanism of the alginate-humic acid mixture was dependent with the permeate flux and alginate nature, e.g., less pore blocking with more cake layer fouling were present at a higher permeate flux during filtration medium viscosity alginate-humic acid mixture. When intermittent relaxation was employed during crossflow filtration, the presence of humic acid could alleviate medium viscosity alginate fouling. This was attributed by a significant shift of irreversible fouling to reversible cake layer fouling, which was readily removed by shear force during relaxation. A comparison of membrane performance during intermittent filtration with periodical flushing using clean water, NaClO (5%), and persulfate (100 mg/L) at 50 °C indicates that high temperature clean water flushing was effective in maintaining membrane performance during filtrating alginate-humic acid complex, which majorly contributed to a reduction of reversible cake layer fouling.