The behavior of uranium and thorium ions in nanofiltration (NF) from aqueous solutions has been studied. It was shown that the retention capacity (R) of the NF membrane for uranium and thorium depends on their state in aqueous solutions. In the case of uranium, the smallest values of R (82–83%) are observed when uranium is in solution as uranyl ions or oxyhydrate complexes at pH in the range from 2 to 6. In solutions with large pH values, the retention of uranium increases (R ≈ 95%) due to the formation of an insoluble U(IV) hydroxide and/or carbonate complexes. In the NF of aqueous solutions of thorium, R grows from 94 to 99% with pH increasing from 1 to 3.5, which is due to the hydrolysis of thorium ions to give oxyhydrate complexes of various compositions. At pH 3–9, the retention of thorium remains constant due to the formation of an insoluble thorium hydroxide. In alkaline solutions (pH > 9), values of R decrease because of the formation of negatively charged hydroxo and/or carbonate complexes. A conclusion is made that the nanofiltration is an effective method for wastewater purification to remove admixtures of uranium and thorium.