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In this paper, we describe an application of mono- and dirhamnolipid homologue mixtures of a biosurfactant as a green agent for destabilisation of a dolomite suspension. Properties of the biosurfactant solution were characterised using surface tension and aggregate measurements to prove aggregation of rhamnolipids at concentrations much lower than the critical micelle concentration. Based on this information, the adsorption process of biosurfactant molecules on the surface of the carbonate mineral dolomite was investigated, and the adsorption mechanism was proposed. The stability of the dolomite suspension after rhamnolipid adsorption was investigated by turbidimetry. The critical concentration of rhamnolipid at which destabilisation of the suspension occurred most effectively was found to be 50 mg·dm−3. By analysing backscattering profiles, solid-phase migration velocities were calculated. With different amounts of biomolecules, this parameter can be modified from 6.66 to 20.29 mm·h−1. Our study indicates that the dolomite suspension is destabilised by hydrophobic coagulation, which was proved by examining the wetting angle of the mineral surface using the captive bubble technique. The relatively low amount of biosurfactant used to destabilise the system indicates the potential application of this technology for water treatment or modification of the hydrophobicity of mineral surfaces in mineral engineering.