In this study, a promising method was developed for the determination of thallium at trace levels by applying chitosan based magnetic solid phase extraction using slotted quartz tube atomic absorption spectrometry. Chitosan based magnetic hydrogels (CMH) were synthesized and used as solid phase extraction sorbents. The variable parameters required for the extraction method such as hydrogel amount, adsorption period and eluent volume were optimized, and under the optimized conditions, limits of detection and quantification values were recorded as 12 and 39 ng/mL, respectively. Real sample applications were performed to test the accuracy of the proposed method. For this purpose, recovery studies were carried out in two different spiking concentrations of thallium in lake water, well water and wastewater samples using the developed extraction/preconcentration method (chitosan magnetic hydrogel based ligandless magnetic solid phase extraction, CMH-LMSPE). The obtained percent recovery values of 87.2-113.2% confirmed the applicability of the method with high accuracy and precision.