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This study reports on the application of biomass derived from the nuisance fresh-water diatom species Didymosphenia geminata towards the adsorption and removal of heavy metal ions from water. The cell-free polysaccharide-based stalks of these diatoms were used as adsorbents to remove harmful metal ions: Pb(II), Ni(II) and Cd(II). Detailed analyses of the adsorption kinetics using both pseudo-first-order model and pseudo-second-order models were performed. The results show a strong correspondence to a pseudo-second-order kinetic model. The Langmuir and Freundlich models were used to describe the adsorption isotherms. The correlation coefficients (r2) of the Langmuir model were equal to 0.994 (Pb2+), 0.995 (Cd2+) and 0.995 (Ni2+), and the correlation coefficients (r2) for the Freundlich model were equal to 0.991 (Pb2+), 0.991 (Cd2+) and 0.987 (Ni2+). The experimental data for all metal ions strongly support the Langmuir isotherm model. It is shown that stalks of D. geminata exhibited exceptional sorption capacity (qm) for Pb(II) ions of 175.48 mg/g. Additionally, a high sorption capacity for Cd(II) (145.86 mg/g), and Ni(II) (130.27 mg/g) was observed. The thermodynamic aspects of the adsorption process of selected metal ions are also discussed. Preliminary tests investigating applications of D. geminata stalks for sewage purification from galvanic industry and battery and accumulator production were performed. These comprehensive studies show that D. geminata can be robustly applied for the removal of harmful metal ions from wastewater.