Membrane filtration is an effective way of separation that usually requires an external driving force. Novel configurations simplifying the filtration process could offer extra versatility and enable separation in a broader context at different scales. This work presents a self-driven 3D filtration strategy based on core–shell polymer composites (CSPCs). The core is a hydrogel sphere that can spontaneously absorb ∼50 times its own weight of water, while a polyamide film, as thin as ∼7 nm, formed through interfacial polymerization serves as the separating shell. These flexible and easy-to-use CSPCs exhibit high-capacity and selective water absorption, which presents unique possibilities for applications such as concentrating biomedical and environmental samples for analyses and recovering valuable resources from waste streams.