The aim of this research was to compare the evolution of head loss in disc (130 µm) and non-woven synthetic fabric filter media used to filter the water in drip irrigation systems. Two forms of treatment of the irrigation water were carried out: one with a chemical product (chlorine) and the other with none. The research used two different filter media: two for each treatment together with a fertigation technique with organic products in both types of treatment. The chemical treatment of the irrigation water was done by chlorination, in which the source of chlorine was sodium hypochlorite. Water from an open reservoir was used, in which a drip irrigation module was installed. The temporal variation in water quality over one year was analyzed, taking into consideration the physical, chemical, and biological parameters of water that can cause clogging problems in emitters. The results showed that, in irrigation water, the pH and iron chemical parameters presented an average risk of clogging, and the hydrogen sulfide parameters presented a high risk. The performance of the filters was analyzed by comparing the concentrations of the effluent on the disc and non-woven synthetic fabric filters in relation to the efffluent's physical and biological parameters. An attempt was made to follow head loss evolution in relation to the volume filtered by the filters so as to make a comparative analysis. It could be seen that the evolution of head loss was more significant and quicker with the non-woven synthetic fabric filter than with the disc filter. The level of clogging in the emitters was calculated by means of a uniform distribution index. The test area using the non-synthetic woven fiber filter presented the smallest level of clogging and the greatest water distribution index.