Proper stewardship of our environment necessitates biodiversity preservation and the wise use of resources. Species that may be pests, such as some algae, may also be used innovatively to mitigate their ecological impact. In this study, we extracted polysaccharide mixtures from three algae-Undaria, Laminaria, and Ulva-under three sets of conditions. The nine extracts contained different polysaccharide compositions and varying carboxylic acid contents. The extracts were converted into their respective algal gels by polyion complex formation with chitosan. The gels were examined for their ability to remove Cu(II) ions from aqueous solutions by ion exchange. The removal efficiency was dependent on the algae extraction conditions, which affected the polysaccharide content of the extracts. Among the gels, those derived from the alkaline extractions of Undaria and Laminaria exhibited higher Cu(II) removal efficiencies than from the other extracts. Gels prepared from extracts with higher uronic acid contents exhibited better removal Cu(II) efficiencies. We expected that an extract’s carboxylic acid content would be proportional to its removal efficiency, because the acidic groups in the polysaccharide bind to the divalent heavy metal ions. However, this proportionality was not observed: extracts that included sulfated polysaccharides were less efficient at ion removal, despite their carboxylic acid content. This can be explained by the structural differences in the adsorption sites between alginate and those of the sulfated polysaccharide. Thus, an environmental deficit was converted into a potential economic benefit in the removal of heavy metals from water.