Extracellular organic matter (EOM) released by algae during algal blooms have been reported to present significant challenges for ultrafiltration (UF) fouling management. However, current understanding of the impact of complex interactions between biopolymers in EOM and the impact of membrane surface properties including pore size and roughness on subsequent fouling behaviour is limited. In this study, EOM from Dolichospermum circinale (DC), two strains of Microcystis aeruginosa (MA555 and MA564), and Chlorella vulgaris (CV), were characterised and filtered with three polyvinylidene fluoride (PVDF) UF membranes. Fouling rate across algal species was found to decrease in the order MA564 > DC > CV > MA555. The high fouling rate of MA564 was attributed to complex carbohydrate aggregation and covalent protein-polysaccharide interactions forming glycoproteins. The biopolymer networks present in MA564 also enhanced fouling reversibility, potentially through electrostatic repulsion interactions with the membrane surface. For DC and MA555, the behaviour of short-term fouling was observed to depend on biopolymer content. Membrane surface roughness influenced the fouling behaviour of DC and MA555, while smaller pore size generally resulted in lower irreversible fouling for all species due to reduced impact of pore blocking. Biopolymers and low molecular weight neutrals (LMWN) were observed to bind to membrane surfaces and pore walls leading to greater chemical cleaning demand for DC and CV, respectively. This study demonstrated the significance of complex biopolymeric interactions elucidated by detailed characterisation methods and the role of membrane pore size and roughness on EOM fouling behaviour towards more effective UF management during algal blooms.