Vineyards in Mediterranean areas suffer from significant soil degradation through erosion, due to rainfall and soil characteristics, as well as soil management practices. Previous studies pointed out the nutrient losses produced by erosion and the benefits that some management practices could have on reducing erosion. This research tried to evaluate the effect of events of different intensities and to assess whether the beneficial effect of compost amendment may pose a potential risk of nutrient loss and environmental pollution in particular under high-intensity events. The study compared soil and nutrient losses in compost-treated and non-treated vineyard soils after rainfall events of different intensities analyzed over 2 years in two vineyards. Runoff samples were collected by triplicate in treated and non-treated soils. Sediment and nitrogen and phosphorous concentrations in the runoff samples were analyzed. The results reveal a reduction in runoff rates and an increase in soil water content in compost-treated soils, which represents a benefit for rainfed vineyards. Both nitrogen and phosphorus losses depended on rainfall characteristics. Although for low intensities there were no significant differences in the amount of nutrient lost by runoff in both treated and non-treated soils, nitrogen and phosphorus losses were higher after high-intensity rainfall events in compost-treated soils. With the expected increase in high-intensity rainfall events associated with climate change in the Mediterranean region, organic amendments should be applied in several splits or incorporated into the soil to avoid increased nutrient loss to water bodies.