The installation location (prepump and postpump) of the filter influences both the head loss and the filtering effectiveness. To understand the difference in the influence, we take the screen filter as the research object, set up two filtration methods and five fertilizer concentrations and then use computational fluid dynamics (CFD) numerical simulations and experiments to compare and analyse the head loss, intercepted volume, particle size and gradation of intercepted impurities of the filter. We also develop calculation methods for the head loss. Our study shows that (1) when the water is clear, the flow velocity in the local upstream surface of the filter under prepump filtration (PRPF) is larger and changes more dramatically. The head loss under PRPF increases by 50%–88% compared to postpump filtration (POPF). (2) When the fertilized solution is applied, more fine particles pass through the filter under PRPF compared to POPF influenced by pump suction, the maximum head loss is reduced by 15%, and the interception volume is reduced by 55%. It follows that fewer fine particles are intercepted. (3) We develop fitting equations for the two filtration methods that reflect the relationship between the head loss and two factors, the relative effective water‐crossing area and the fertilizer concentrations, and R2 > 0.83. The study provides a reference for the installation and utilization of filters in microirrigation systems.