Fucoidanase and alginate lyase are promising biocatalysts for several biotechnological applications. The sequentially extracted fucoidan and alginate from the brown macroalgae Sargassum latifolium were used for the optimization of a cost-effective culture medium for fucoidanase and alginate lyase production by the marine fungus Dendryphiella arenaria. Plackett–Burman statistical design was conducted for initial determination of the importance of 11 independent variables on enzyme potentiation, and the significant variables were further optimized using Box–Behnken design. The optimum conditions for fucoidanase production were fucoidan (1.5% w/v), NaCl (1.5%), urea (0.3%), and incubation period (2 days), which gives ~ 4 U mL−1 of crude fucoidanase. While, alginate (1.5% w/v), NaCl (4%), NH4Cl (0.3%), and incubation period (6 days) were the optimum conditions that enhanced alginate lyase production to ~ 24 U mL−1. Additionally, a new protocol for the enzymatic saccharification of fucoidan and alginate was optimized using Box–Behnken design with respect to substrate concentration, enzyme dosage, and temperature. The enzymatic saccharification of citric acid-extracted fucoidan gave a maximum yield of reducing sugar 365 mg g−1 fucoidan, while the alkali-extracted alginate gave 439.66 mg g−1 alginate. The results showed that the two enzymes could be exploited for the efficient production of reducing sugars from fucoidan and alginate, which are the key substrate for producing biofuels from brown macroalgal biomass.