Sand filters are gradually being adapted for use in the water treatment. The hydraulic performance of the filter bed directly affects the pollutant removal performance. Tracer experiments and residence time distribution (RTD) theory were used to characterize the flow in a special upflow sand bed filter. The detailed flow pattern of the reactor was obtained from computational fluid dynamics (CFD) simulation. An orthogonal analysis was adopted to optimize the filter's structures, including the piping network, free-water surface and bearing-layer. The RTD study and CFD simulation show that the free-water surface and the bearing-layer have the functions of collecting and distributing water, respectively. The free-water surface and the bearing-layer have little effect on the flow pattern when the network is distributed throughout the water-carrying section. However, when the piping network is distributed in the partial carrying section, the free-water surface and the bearing-layer can improve the hydrodynamics as well as eliminate preferential/shortcut flow and stagnant volume. The orthogonal analysis shows that the order of factors with regard to the effect on volume efficiency is as follows: bearing-layer > free-water surface > piping network. There are marked interactions between the factors. The reactor with partially piping network, free-water surface and bearing-layer had the highest volume efficiency. The flow pattern is close to plug flow and the normalized mean retention time is 1.093. Increasing the packing medium diameter in the fully piping network reactor greatly decreases the unavailable volume, while the diameter in partially piping network reactors does not significantly change the water flow pattern in reactors.