The seaweed Cystoseira trinodis was fermented by different fungi prior to extraction of fucoidan and alginate to enhance their antioxidative potential. All the investigated fungi were able to produce fucoidanase (1.05–3.41 U/ml) and alginate lyase (7.27–18.59 U/mL). Different fungal species induced a reduction in the molecular weight (MW) of fucoidan and alginate in comparison to the unfermented control. The MW of fucoidan reduced by 41–81.5%, while the MW of alginate was reduced by 28–75%, depending on the fungal species. Significant increases in the fucose and sulphate contents of fucoidan and mannuronic/guluronic acid ratio of alginate were induced by fungal fermentation. Fungal pretreatment enhanced the ferric reducing antioxidant power, total antioxidant capacity and hydroxyl radical scavenging activity of both fucoidan and alginate. Additionally, enzymatic pretreatment of the macroalgal biomass assisted in the recovery of fucoidan and alginate with low molecular weight and enhanced antioxidative potential.