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In irrigated semi-arid areas, nutrient pollution from agriculture from irrigation return flows is one of the most important surface water quality problems and can lead to eutrophication. In this study, a new phosphorus index called IPreg has been adapted as a management tool for application to irrigated farming systems and then applied within Las Filadas’ drainage basin (Spain) at a plot scale. Two new transport factors related to the irrigation management system were introduced: (i) the seasonal irrigation performance index and (ii) the efficiency of the mean irrigation dose that represents average water losses below the root zone when an average irrigation dose is applied. IPreg includes 10 factors, three of which account for P availability in the soil and seven for P transport processes. The results indicate that 18% of the study area had a high to very high risk of phosphorus loss and 60% at medium risk. Corn and alfalfa had the highest IPreg values under intense irrigation and high fertilizer application rates. IPreg was also higher in phosphorus-rich soils and in plots treated with organic manure, especially pig slurry.