Traditional cell culturing methods are limited in their ability to supply growth medium to cells within scaffolds. To address this, we developed a custom perfusion bioreactor that allows for dynamic medium supply to encapsulated or seeded cells. Our custom-designed bioreactor improves the in vivo stimuli and conditions, which may enhance cell viability and proliferation performance. Some of the efforts include using dual medium tanks to replace the medium without stopping perfusion and a newly designed perfusion chamber that can accommodate an array of cassettes allowing for a wide assortment of scaffold shapes and sizes. In this paper, we explored the response of fluid flow to certain types of scaffold pore geometries and porosities using simulation and experimental approaches. Various pore geometries were considered, such as uniform triangular, square, diamond, circular, and honeycomb having uniform and variable sizes. Finally, bone tissue architecture was mimicked and simulated to identify the impact of fluid flow. Based on the results, optimum pore geometry for scaffolds were determined. We explored real-time fluid flow response on scaffolds fabricated with 8% Alginate, 4% Alginate-4% Carboxymethyl Cellulose (CMC), and 2% Alginate-6% CMC incubated, allowing a constant fluid flow for various periods such as 1, 2, 4, and 8 h. The change of fabricated scaffolds was determined in terms of swelling rate, i.e., change of filament width and material diffusion, i.e., comparison of dry material weight before and after incubation. This comparative study can assist in application-based materials selection suitable for incubating in a perfusion bioreactor.