Clay minerals are widely used as excipients and active ingredients in cosmetic products and pharmaceutical preparations. An important factor for this application is the purity of clay minerals. In nature clays often contain carbonates - calcite and dolomite. Calcium and magnesium ions released from carbonates behave as cementing agents and cause aggregation of clay particles. Because of these clay aggregates the purification of raw clay samples from non-clay minerals is hindered. The removal of carbonates can be performed by dissolution with organic and inorganic acids. The aim of this study is to evaluate the changes in the aggregation of clay particles after complete removal of carbonates with different organic acids. Comparing with untreated clay, the overall stability of clay water suspensions has increased. Although in the dissolution process of the carbonates soluble and insoluble calcium and magnesium salts are formed as by-products, the XRD analysis shows only calcium oxalate.The removal of carbonates decreases the aggregation process of clay particles. Therefore it is possible to improve the isolation of clay minerals from raw clay samples.