The extracellular matrix (ECM) that surrounds cells in vivo represents a biological barrier for nanomaterials in biomedicine. Herein, we present a system for investigating the interactions between circulating polymer particles and ECM components in vitro using a commercially available flow-based device. We use this system to show how material-dependent interactions of two different particle types-one assembled using poly(ethylene glycol) (PEG) and one prepared using poly(methacrylic acid) (PMA)-affect their interactions with basement membrane extracts during in vitro circulation, with PEG particles remaining in circulation longer than PMA particles. Further, by comparing macroporous hyaluronic acid gel constructs (typically used for tissue engineering) with basement membrane extracts, we show that scaffold-effects (porosity and surface chemistry) impact on circulation time in vitro. The presented system is simple and modular, and can be used to rapidly screen fundamental interactions of engineered particles with biologically relevant microenvironments under flow-conditions.