The transportation and distribution of living bacteria particles were analyzed in a computational fluid model with the mobile phase of human urine, which resembles the pathogenesis of bacterial urine tract infections with complications of urethral calculi. Interrelated processes contributing to the mass transport and bacteria growth in the urine flow were evaluated. The two-dimensional model was also solved computationally. The results reflected that a urethral calculus could bring about the backward dispersal of bacteriuria in the case of urine tract infection. Furthermore, the shape of urethral stone is an important factor in the biofilm development on its surface. We also designed the conceptual experimental system for in-vitro simulation and further verification, composed of a cell-based lab-on-a-chip and the photomultiplier-tube (PMT)-based bioluminescent detection module.