We report an approach to fully visualize the flow of two immiscible fluids through a model three‐dimensional (3‐D) porous medium at pore‐scale resolution. Using confocal microscopy, we directly image the drainage of the medium by the nonwetting oil and subsequent imbibition by the wetting fluid. During imbibition, the wetting fluid pinches off threads of oil in the narrow crevices of the medium, forming disconnected oil ganglia. Some of these ganglia remain trapped within the medium. By resolving the full 3‐D structure of the trapped ganglia, we show that the typical ganglion size, as well as the total amount of residual oil, decreases as the capillary number Ca increases; this behavior reflects the competition between the viscous pressure in the wetting fluid and the capillary pressure required to force oil through the pores of the medium. This work thus shows how pore‐scale fluid dynamics influence the trapped fluid configurations in multiphase flow through 3‐D porous media. © 2013 American Institute of Chemical Engineers AIChE J, 59:1022‐1029, 2013