This study re-examines the role of calcium ions ( \({Ca}^{2+}\) ) in pyrite flocculation using acrylamide-based flocculants (A26 and A27), combining experimental and molecular dynamics (MD) approaches. Contrary to conventional wisdom, results demonstrate that \({Ca}^{2+}\) adversely influences flocculation efficiency. Laboratory tests showed that increasing \({Ca}^{2+}\) concentrations (up to 150 mg/L) reduced settling velocities by up to 50% and increased turbidity, with the high-acrylamide flocculant A27 being particularly affected. MD simulations revealed that \({Ca}^{2+}\) neutralizes negative charges on both pyrite surfaces and flocculant polymers, weakening critical hydrogen bonding and electrostatic interactions. This disruption caused a 2 Å shift in flocculant adsorption position and decreased floc density by 15–20%, leading to less stable aggregates. Performance depended strongly on flocculant composition: A27 (17:1 acrylamide: acrylic acid ratio) outperformed A26 (9:1 ratio) due to enhanced hydrogen bonding, but both suffered efficiency losses with \({Ca}^{2+}\) . Optimal flocculation occurred at pH 10.5 without \({Ca}^{2+}\) , where A27 achieved 142.07 m/h settling velocity. FTIR analysis confirmed electrostatic interactions dominated the adsorption mechanism, with no evidence of \({Ca}^{2+}\) bridging. These findings challenge established paradigms about \({Ca}^{2+}\) ’s beneficial role and provide molecular-level insights for optimizing flocculant design in mineral processing, particularly for \({Ca}^{2+}\) -rich systems. The study highlights the need to reconsider water treatment strategies in mining operations where calcium concentrations may compromise flocculation performance.