Pesticides enter to water sources not only from agricultural lands, but also from wastewaters of the enterprises, when they are produced and packed. Pressure-driven membrane processes allow one to remove pesticides from water simultaneously with their concentrating, further the concentrate can be used as a commercial product. In this work, polymer-inorganic membranes have been developed for this purpose, which is achieved by the formation of nanopores in commercial micro- and ultrafiltration membranes by means of embedding nanoparticles of hydrated zirconium dioxide (10–100 nm). Modifying changes porous structure of the membranes due voids between nanoparticles and also due to hydrolysis of polymers during the synthesis procedure. A size of rejection-determining pores is 4–31 nm. The nanoparticles are located on the upper part of active layer of the membranes preventing their fouling. The membranes were tested with solutions of dicamba, nicosulfuron, pendimethalin and tebuconazole. Sequential low-pressure filtering through the membranes and biochar bed decreases their content in water down to the maximal allowable concentration and lower. The concentrate can be used further as a commercial product.