The use of effluent for irrigation could affect the chemical and hydraulic properties of soils due to its high salt and organic matter (OM) content, and, consequently, the rainfall–infiltration–runoff–erosion relationships during the subsequent rainy season. This study investigates the effects of long-term effluent irrigation on soil chemical properties, seal formation, infiltration, and soil loss under rainfall. Simulated rainfall (85 mm) was applied to (i) air-dried or (ii) prewetted clay and sandy soils from plots that had been irrigated with fresh water (FW) or effluent for >10 yr. Effluent irrigation increased the total OM content and the exchangeable sodium percentage (ESP) of the soils. The cumulative infiltration in FW- and effluent-irrigated clay soils was 6.5 and 5.6 mm, respectively, in the initially dry soils, and 52.3 and 51.5 mm, respectively, in the prewetted soils. In the FW- and effluent-irrigated sandy soils, the corresponding values of cumulative infiltration were 79.5 and 44.7 mm, and 85.0 and 56.3 mm, respectively. In the sandy soil, the higher sodium adsorption ratio (SAR) values in the leachate of effluent-irrigated soil led to greater clay dispersion, which enhanced seal formation, reduced infiltration, and increased soil loss. In the clay soil, slaking was the main process involved in seal formation, neglecting the possible deleterious effect of effluent irrigation. When slaking was prevented, the SAR values in the leachate of the effluent-irrigated soil decreased during rainfall and were similar to those of the FW-irrigated soil at the end of the applied rainfall amount. This was probably due to the exchange of adsorbed Na with soluble Ca, which minimized the differences in clay dispersion, infiltration, and soil loss. Therefore, in the clay soil, aggregate slaking might be the main process involved in seal formation and affecting infiltration and erosion. These results show that the effect of effluent irrigation on infiltration, runoff, and soil loss depends on the soil type (amount of clay and CaCO3) and the dominant mechanisms of seal formation. Therefore, to prevent a possible deleterious effect on soil structure, it is necessary to identify sensitive areas and soils before the application of effluents for irrigation.