A new method for the study of pathogen transport in porous media is presented. The method is based on conjugation of fluorescent dyes to target bacteriophages and application of the modified bacteriophages for tracer studies. We demonstrate that the relevant transport determining properties of Rhodamine and several fluorescein-labeled phages are practically identical to those of the native bacteriophages. The advantages of the proposed method relative to direct enumeration of bacteriophages by plaque forming unit method, turbidity, fluorescent microspheres, and other alternative tracers are discussed. Notable advantages include simple quantitation by optical methods, unbiased signals even when virus aggregates are formed, and the ability to decouple inactivation kinetics from transport phenomena. Additionally, the signal reflects the removal and transport of the studied microorganism and not a surrogate.