Macroalgae cultivation shows potential for the application as emerging feedstock for microbial fermentation to produce biochemicals. However, metal residues in macroalgae might affect the fermentation capacity of relevant microorganisms. This aspect is currently not considered when selecting macroalgae and microorganism species for microbial fermentation. To consider this aspect for selecting viable macroalgae and microorganism species, we link metal exposure in bioreactors from macroalgae residues to ecotoxicological test results for relevant microorganisms. Our results indicate that estimated bioreactor concentrations for most metals are below microorganism effect levels. For copper and hexavalent chromium, however, reactor concentrations might exceed relevant effect levels for at least some considered microorganism species. Adjusting water hardness in the bioreactor as well as selecting algae harvest location and macroalgae species might minimize metal exposure to fermenting microorganisms, in support of optimizing the biorefining process for biochemical production.