A large number of industries use heavy metal cations to fix dyes in fabrication processes. Malachite green (MG) is used in many factories and in aquaculture production to treat parasites, and it has genotoxic and carcinogenic effects. Chromium is used to fix the dyes and it is a global toxic heavy metal. Face centered central composite design (FCCCD) has been used to determine the most significant factors for enhanced simultaneous removal of MG and chromium ions from aqueous solutions using marine green alga Enteromorpha intestinalis biomass collected from Jeddah beach. The dry biomass of E. intestinalis samples were also examined using SEM and FTIR before and after MG and chromium biosoptions. The predicted results indicated that 4.3 g/L E. intestinalis biomass was simultaneously removed 99.63% of MG and 93.38% of chromium from aqueous solution using a MG concentration of 7.97 mg/L, the chromium concentration of 192.45 mg/L, pH 9.92, the contact time was 38.5 min with an agitation of 200 rpm. FTIR and SEM proved the change in characteristics of algal biomass after treatments. The dry biomass of E. intestinalis has the capacity to remove MG and chromium from aquatic effluents in a feasible and efficient manner.