Modifying the properties of bio-based materials has garnered increasing interest in recent years. In related applications, the ability of alginates to complex with metal ions has been shown to be effective in liquid-to-gel transitions, useful in the development of foodstuff and pharma products as well as biomaterials, among others. However, despite its ubiquitous use, alginate behavior as far as interactions with cations is not fully understood. Hence, this study presents a detailed comparison of alginate's complexation with Na+ and Ca2+ and the involved intramolecular hydrogen bonding and biomolecular chain geometry. Using all-atom molecular dynamics simulations, we find that in contrast to accepted models, calcium cations strongly bind to alginate chains by disruption of hydrogen bonds between neighboring residues, stabilizing a left-hand, 3-fold helical chain structure that enhances chain stiffness. Hence, while present, the traditionally accepted egg-box binding mode was a minor subset of possible conformations. For a single chain, most of the cation binding occurred as single-cation interaction with a carboxyl group, without the coordination of other alginate oxygens. The monovalent Na+ ions were found to be mostly nonlocalized around alginate and therefore do not compete with intramolecular hydrogen bonding. The different binding modes observed for Na+ and Ca2+ contribute toward explaining the different solubility of sodium and calcium alginate.