Protozoa are important in environmental biotechnology and play a critical role in public health. Most protozoan habitats are a mosaic of physically and biologically distinct microenvironments on a spatial scale of millimeters to micrometers. Such heterogeneity strongly affects protozoa in the environment. However, it is difficult to replicate and observe the effects of micro-scale heterogeneity using conventional experimental techniques. The objective of this research is to provide a clearer understanding of the effects of micro-scale physical and biological heterogeneity on protozoan migration in porous media. Microfluidic devices with well-defined microstructural features are designed to mimic the physical complexity of real microbial habitats. Protozoan migration behaviors at the pore scale, including location of channel openings and navigation along narrow passages, have been directly observed. The motility of protozoa in narrow channels has also been measured. With the presence of bacteria, protozoa have also shown strong migration selectivity for channels containing live bacteria (versus control channels) and exhibited a periodic migration pattern. The empirical results and qualitative observations resulting from this research will be helpful in defining the physical limitations on protozoan grazing in porous media and understanding the mechanisms involved in protozoan prey-sensing and other pore-scale processes that are critical to microbial community functions in natural and engineered systems.