To reduce disease impact, Philippine farmers developed the green-water (GW) system, which has been spreading rapidly since 2008. In the most applied GW-system, the shrimp pond receives water from a reservoir stocked with tilapia. We collected financial data on GW and non-GW systems from farms having similar management and environmental context. All farms had more than one pond; the average pond area was <1 ha, and total pond areas per farm ranged from 1.4 to 139 ha. The total variable and fixed costs per ha of shrimp pond were not different for GW and non-GW farms, but on GW farms the cost per kg of shrimp produced was lower. The latter was higher than the 2009 market price of 30 g shrimp for non-GW farms mainly. In GW farms the cost of seed was lower, and survival rates and individual shrimp weights at harvest were higher for an equally long culture period.