The absorption of dietary calcium through the intestinal barrier is essential for maintaining health in general and especially of the bone system. We propose a microfluidic model that studies free calcium (Ca2+) transport through a confluent monolayer of Caco-2 cells. The latter were cultured on a porous membrane that was positioned in between a top and bottom microfluidic chamber. Fresh cell culture medium was continuously supplied into the device at a flow rate of 5 nL s−1 and the culture progress of the cell monolayer was continuously monitored using integrated Transepithelial Electrical Resistance (TEER) electrodes. The electrical measurements showed that the Caco-2 monolayer formed a dense and tight barrier in 5 days. The transported free Ca2+ from the top microfluidic chamber to the basolateral side of the cell monolayer was measured using the calcium-sensitive dye fura-2. This is a ratiometric dye which exhibits an excitation spectrum shift from 340 nm to 380 nm, when it binds to Ca2+ with an emission peak at 510 nm. Therefore, the concentration of free Ca2+ is proportional to the ratio of fluorescence emissions obtained by exciting at 340 nm and 380 nm. The barrier function of the cell monolayer was evaluated by a measured rate of Ca2+ transport through the monolayer that was 5 times lower than that through the bare porous membrane. The continuous perfusion of cell nutrients and the resultant mechanical shear on the cell surface due to the fluid flow are two key factors that would narrow the gap between the in vivo and in vitro conditions. These conditions significantly enhance the Caco-2 cell culture model for studying nutrients bioavailability.