A system for sorting and trapping magnetic target species includes a microfluidic trapping module designed to receive and then temporarily hold magnetic particles in place within the module. The magnetic particles flowing into the module are trapped there while the other sample components (non-magnetic) continuously flow through and out of the station, thereby separating and concentrating the species captured on the magnetic particles. The magnetic particles and/or their payloads may be released and separately collected at an outlet after the sample passes through the trapping module.