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Using copper (II) ion as a model pollutant, we report a new bioremediation concept, which involves the use of green algae Chlamydomonas reinhardtii to efficiently collect copper ions from the solution, followed by encapsulating copper loaded algae with silica, thus reducing the bioavailability of copper ions in the solution. Specifically, the potential of Chlamydomonas reinhardtii as an active copper (II) absorbent was demonstrated by quantifying and characterizing the copper uptake rate, capacity, efficacy, as well as copper retention from C. reinhardtii. Subsequently, a method of encrusting copper loaded C. reinhardtii with silica was developed, taking the advantage that the presences of high abundant polysaccharides and glycoproteins on the cell walls, as well as the presence of (3-amino-propyl) trimethoxysilane (APS) can function as nucleation center for silicification process of tetramethyl orthosilicate (TMOS). Both fluorescence imaging and scanning electron microscope (SEM) imaging confirmed the silica encrustation. It is expected that silica encrustation of algae has the potential for in situ remediation of various contaminants in a wide range of environments while providing long-term stabilization and diminishing the bioavailability of the contaminants.