A magnetic particle separation system includes a magnetic field generating device having an upper surface with a receiving area formed thereon; and a magnetic field generating element disposed beneath the upper surface, the magnetic field generating element being configured to produce a magnetic field above the upper surface. A container assembly is disposed on the upper surface and includes: a flexible container having an outer wall with an interior surface that at least partially bounds an internal compartment, the outer wall having a front side and an opposing back side with the internal compartment disposed therebetween; a fluid inlet extending through the outer wall at the front side; a fluid outlet extending through the outer wall at the front side; and a first partition projecting into the internal compartment from the front side between the fluid inlet and the fluid outlet.