Thorium is a weak radioactive element, but the control of its concentration in natural aqueous systems is of great interest for health, because it is a toxic heavy metal. The present paper presents the recovery of thorium from diluted synthetic aqueous systems by nanofiltration. The membranes used for the nanofiltration of systems containing thorium species are composites containing 4′-Aminobenzo-15-crown-5 ether (ABCE) and sulfonated poly–etherether–ketone (sPEEK). The composite membranes (ABCE–sPEEK) were characterized by scanning electron microscopy (SEM), energy-dispersive X–Ray spectroscopy (EDAX), thermal analysis (TG and DSC), and from the perspective of thorium removal performance. To determine the process performance, the variables were the following: the nature of the composite membrane, the concentration of thorium in the aqueous systems, the rotation speed of the stirrer, and the pressure and the pH of the thorium aqueous system. When using pure water, a permeate flux value of 12 L·m−2 h−1 was obtained for the sPEEK membrane, and a permeate flux value of up to 15 L·m−2 h−1 was obtained for the ABCE–sPEEK composite membrane. The use of mechanical stirring, with a propeller stirrer, lead to an increase in the permeate flux value of pure water by about 20% for each of the studied membranes. Depending on the concentration of thorium and the pH of the feed solution, retentions between 84.9% and 98.4% were obtained. An important observation was the retention jump at pH 2 for the ABCE–sPEEK composite membrane. In the paper, a thorium ion retention mechanism is proposed for the sPEEK membrane and the ABCE–sPEEK composite membrane.