The input-intensive rainfed tropical ecosystem, where wet season (WS) rice (Oriza sativa L.)-dry season (DS) diversified high-value upland crops like vegetables predominate, has resulted in a problem of a large leakage of N into the environment, thereby polluting the water. Excessive use of N fertilizer in high-value crops grown in DS is economically motivated. Out of twenty water sources evaluated in a watershed with a total area of 265 ha located in Magnuang, Ilocos Norte, Philippines, twelve had near or above the World Health Organization's (WHO) NO3-N limit for drinking water of 10 ppm. Soil mineral N (upper 100 cm) observed in seven rice-sweet pepper (Capsicum annuum L.) farmers' fields ranged from 111 to 694 kg ha(-1) which decreased by 10 to 68% in plots with dry-to-wet (DTW) crops like indigo, indigo+mungo and corn. In fallow plots where mineral N was either maintained or increased, it showed movement to lower soil profiles demonstrating NO3 leaching without a crop. On average, maize (Zea mays L.) captured 176 kg N ha(-1) and indigo (Indigofera tinctoria L.) 194 kg N ha(-1). In both fallow and planted plots, mineral N declined to low levels at 100% water-filled pore spaces (WFPS) before rice transplanting. A strategy for including indigo plus maize as a N-catch crop is proposed to decrease NO3 leaching and maximize N use efficiency in a rice-sweet pepper cropping system.