Due to their small size, high diffusivity, and chemically active surfaces, nanoparticles share much in common with water-soluble proteins. These similarities have generated great interest in using biofunctional nanoparticles as a route to deliver targeted therapeutics. Already nanoparticles have found applications in the hyperthermia of tumors, personal care lotions, and tissue scaffolding. Our study focuses on the targeting of such nanoparticles to specific biological sites. It therefore seeks to identify the factors that control the migration and capture of nanoparticles within living systems. In particular, we examine the affinity of anti-collagen coated magnetite nanoparticles for collagen IV-coated surfaces under flow stress. The studies are performed within microfluidic devices that are designed to mimic various fluid flow patterns within the body. We find, in this case, a large background signal due to nonspecific binding. Further examination shows a correlation between chemical functionality (e.g., surface charge, hydrophilicity) that suggests that a balanced approach between biological functionality and chemical functionality may reduce the background from nonspecific binding to acceptable levels.