Stahphylococcus epidermidis and klebsiella pneumoniae are examples of bacteria that produce an extensive network of polysaccharides that lead to formation of a biofilm as an exterior capsule to the cellular pathogen. This extracellular matrix helps to create a protective environment in which the bacteria can proliferate. The extracellular structure of biofilm aggregates can anchor to biomedical devices, such as catheters, leading to bloodstream infection. The shedding of these aggregates into the blood stream and their behavior and fate in the circulatory system is hypothetically linked to the rheological response of the capsular aggregates. However, mechanical rheology measurements on these materials are challenging because of sample volume requirements and material heterogeneity. Thus, we have produced a microfluidic device to determine the rheological response of biofilm aggregates on scales relevant to the circulatory system. The device uses flexible valves fabricated in poly(dimethyl siloxane) according to the methods of Struder and co-workers (Struder V, Hang G, Ortiz M, Anderson WF and Quake SR, J. Appl. Physics 95(1), 393-398, 2004) to deform bacterial aggregates grown at biologically relevant shear rates in the microfluidic environment. We find that the response of the valve membrane is correlated with the elastic properties of the material loaded into the device. This response is measured in a model material, gellan gum, using microrheological particle tracking of polystyrene spheres suspended in the elastic matrix. The particle trajectories are compared with the results of finite element simulations using linearly elastic constitutive models. The approach of comparing between microrheology and finite element simulation is extended to probe the local elastic response of biofilms of varying intra and extracellular structure through genetic modification of the pathogens.