Microscopic diatoms, unicellular algae that are abundant in the earth’s waters, have been interesting to researchers because of their unique outer shell structure known as frustules. The frustules are composed of amorphous silica, naturally nano-fabricated, while displaying unparalleled diversity in structure and morphology. The nanoporous structures of the frustules allow them to be used for specialized filtration procedures. These diatom frustules however haven’t been fully characterized for fluid/particle flow. Each diatom frustule contains two to three porous layers. The inner layer of Coscinodiscus sp. for instance has holes of around 1.2 µm and the outer layer comprises holes of around 300 nm diameter. This research presents diffusion studies to characterize the flow of particles through these frustule pores. In order to successfully carry out the diffusion studies, a single frustule of diatom was stuck onto the end of a hollow capillary fibre with internal diameter of 15.5 µm. The capillary was then inserted into 500 µm glass tube filled with fluorescent dye, Rhodamine B, and the experiment carried out with Nikon epifluorescence microscopy. We observed that diffusion through the inner layer was affected by its porosity resulting in the reduction of the diffusivity i.e. D = 1.1×10-10 m2/s. The diffusion through both the inner and outer layer however resulted in diffusion coefficient (D = 3.1×10-11 m2/s) that was influenced not only by the porosity but also the tortuosity. Thus we notice that the intricate three dimensional structure of the diatom imposes different boundary conditions to the flow of the Rhodamine B molecules resulting in different diffusion rate.