Abstract: Surface runoff and subsurface flow patterns were monitored in hillside runoff plots in almond and olive orchards with soils covered with spontaneous plants over two hydrological years. The experimental runoff plots were located on the south flank of the Sierra Nevada (Lanjarón, SE Spain) at 580 m a.s.l. with an area of 40 m2 (10 m × 4 m). The surface and subsurface discharge were collected and measured at different soil depths (0, 5, 10, 25, and 50 cm), and the dissolved nutrient concentrations (NO3–N, NH4–N, PO4–P, and K) were determined. According to the findings, the subsurface flow pathways drained most of the rainfall water compared with surface runoff, which was affected by plant cover. The influence of rainfall intensity (I30) on surface runoff was more meaningful than that on subsurface flow. Throughout the monitoring period, the runoff coefficients at soil depths of 0, 5, 10, 25, and 50 cm averaged 0.04, 0.11, 0.14, 0.17, and 0.18, respectively. Subsurface flow was one of the dominant pathways for N and K loss, whereas P loss mainly occurred via surface runoff. Moreover, the concentrations in subsurface flow were higher than the recommended level for standard water quality for NO3–N, NH4–N, and PO4–P. Subsurface flow was the main route of dissolved nutrient delivery, making these nutrients available to the root systems of trees, where nutrient uptake is more likely to occur. Thus, by lessening surface runoff and encouraging surface vegetation coverage to facilitate the recycling of nutrients and buffer the rainfall’s impact on the soil surface, nutrient loss control can be achieved.