Kidney failure is a common disease prevailing in the present generation. Renal disfunction inflict adverse effects on human health that are much fatal. Kidney failure has attracted great attention among the present scientific community. Thus, it is desirable to develop an implantable device to replace the failed kidney that could be partially possible with Kidney-on-Chip technology. This paper presents a Kidney-on-Chip model where size-dependent re-absorption of the kidney is majorly investigated by considering the implications of hydrostatic pressure. The device is comprised of two blood tubules separated by a main tubule in the Centre. The main tubule connects both the blood tubules by the means of transporting channels. The transporting channel allows the flow of solutes from the main tubule to blood tubules depending on size of the solutes. The hydrostatic effect can alter the functioning of the kidney by effecting the cytoskeleton arrangement of kidney cells. Employing hydrostatic effects into the device will make the model more compact and realistic. The analysis was made by employing hindrance in the form of bars arranged in zig–zag fashion in the main tubule forming stepwise structure. Simulation results of presented design have produced an outflow velocity of 9.12 × 10−5 m/s which is greater than 8.2 × 10−5 m/s without hydrostatic effect. The re-absorption rate has been improved from 50 to 55% which is desirable. The mathematical analysis was made to support the simulation results. Different studies were conducted on the device performance by changing the parameters that affect fluid flow such as inflow velocity, density, viscosity, capillary forces, and surface tension. The presented work can produce a bio-reactor for kidney-on-Chip applications with more realistic results. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.