This study simulated the biophysical, economic and environmental implications of cowpea fertigated with human urine (equivalent to 60 kg N ha-1) as source of organic N. The DSSAT CROPGRO model was used to simulate harvested cowpea yield, N (leached) , N (uptake) , monetary returns or gross margins in ($) under two different treatments: without fertigation or human urine (T 0) and with fertigation (T 1). Biophysical analysis using the Cumulative Probability Distribution (CPD) showed a 50% probability of the harvested cowpea yield under T 1 being higher than under T 0 at 1060 and 600 kg ha-1 respectively, accounting for a 43.4% difference. The Mean Gini Stochastic Dominance (MGSD) analysis was used to assess the gross margin and helped in deciding on the best strategic and management option. The findings of this study revealed a 50% probability (CPD 0.5), of higher gross margin under T 1 at $-215 higher than under T 0 at $285. This was a $70 difference per season under T 1 and so enhancing a faster payback and a larger monetary return on overall investments. Similarly, seasonal analysis with fertigation showed that at CPD 0.5 , the N (leached) was still < 4 kg N ha-1 per season and so posed no environmental risks. The simulation results also showed higher a probability of N (uptake) of about 270 kg N ha-1 during fertigation compared to about 95 kg N ha-1 under T 0. Therefore, the DSSAT CROPGRO model can be used to successfully forecast future cowpea yields, gross margin, N (leached) , N (uptake) under different management practices to enable smallholder farmers in South Sudan make informed decisions on sustainable cowpea production.