The magnetic resonance microscopy (MRM) work at Montana State University has extended the imaging of a single biofilm in a 1 mm capillary reactor to correlate T 2 magnetic relaxation maps displaying biofilm structure with the corresponding velocity patterns in three dimensions in a Staphylococcus epidermidis biofilm fouled square capillary. A square duct geometry is chosen to provide correlation with existing experiments and simulations, as research bioreactors tend to be of square or rectangular cross section for optical or microelectrode access. The spatially resolved velocity data provide details on the impact of biofilm induced advection on mass transport from the bulk fluid to the biofilm and through the capillary bioreactor. These issues are of significant importance in biosensor and bioseparations applications based on microfluidics or 'lab on a chip' technology, as well as a model for a flow in fractured geological media. Extension of published work in Journal of Magnetic Resonance applied concepts from the theory of fluid mixing to quantify the secondary flows induced by the spatially heterogeneous biofilm. The secondary flows are measured to be 20% of the axial velocity and indicate a significant alteration of transport from the bulk fluid to the biomass from diffusive to convective dominated. A paper has been published in Biotechnology and Bioengineering detailing the experimental results and analysis. The impact of microbial activity, particularly surface attached biofilms, on the transport of fluids in porous systems is relevant to fields as seemingly diverse as geophysics and medicine. Few direct experimental data on the impact of bioactivity on transport dynamics in three-dimensional media are available due to sample opacity. Non-invasive magnetic resonance microscopy (MRM) directly measures length and time scale dependent dynamics in porous media. Our research demonstrates by direct measurement of the propagator, i.e. the displacement conditional probability or van Hove scattering function, the transition from normal to anomalous hydrodynamic dispersion as a function of bioactivity. The microbial activity transforms the porous media from a homogeneous to heterogeneous structure, increasing system complexity as defined in terms of dynamics. Continuous time random walk (CTRW) based fractional advection-diffusion equation (ADE) models which generate anomalous or fractional dynamics are compared to the measured dynamics in both the propagator displacement space and the Fourier reciprocal displacement wavelength space. The data provide insight into the application and development of fractional calculus based models and indicates their direct applicability to biofilm impacted porous media transport. A manuscript reporting these results was published in Physical Review Letters. Unsaturated flow in porous media has been analyzed using magnetic resonance (MR) propagator measurements of scale dependent displacement. The data show a change in dynamics from Gaussian to non-Gaussian. Velocity and pore distrib...