We show experimentally that a flow-induced, Reynolds number-dependent particle-capture mechanism in branching junctions can be enhanced or eliminated by varying the junction angle. In addition, numerical simulations are used to show that the features responsible for this capture have the signatures of classical vortex breakdown, including an approach flow aligned with the vortex axis and a pocket of subcriticality. We show how these recirculation regions originate and evolve and suggest a physical mechanism for their formation. Furthermore, comparing experiments and numerical simulations, the presence of vortex breakdown is found to be an excellent predictor of particle capture. These results inform the design of systems in which suspended particle accumulation can be eliminated or maximized.