Several recent publications report the use of low-cost and locally available adsorbents in biopurification systems to eliminate pesticides from water. Nonetheless, the literature is insufficient to cover this problem, and more investigations are needed in this field to evaluate the possible application of economical adsorbents to prevent pesticide water resources contamination caused by direct losses. This study focuses on the fate of endosulfan metabolites, in small-scale biopurification systems, using as adsorbents treated and untreated organic agricultural stones (date, olive and avocado). The effects of sorbent particle size, adsorbent dose, contact time, concentration of pesticide solution and temperature on the adsorption processes were systematically studied in batch experiments. Pesticide determination was carried out using stir bar sorptive extraction and gas chromatography coupled with mass spectroscopy. Maximum removal efficiency (94.8%) was reached for endosulfan sulfate (0.1 mg L −1) using the acid-treated date stones (ATOS) fraction <125 μm (solid/liquid ratio: 1 g L −1). According to the general behavior of the adsorption mechanism, date stones show the higher removal efficiency followed by olive and avocado stones, respectively. The analyses of the results reveal that the thermo chemical treatment improves notably the pesticides adsorption efficiency of the studied sorbents and that the adsorption decreases when the pesticide solubility rises. Experimental adsorption data were analyzed according to various kinetic models. Lagergren and Morris–Weber equations were applied to fit the kinetic results. The second order model was the most suitable and intra-particle diffusion was found to be the rate controlling the adsorption process.