Many proponents of organic farming claim that it is a sustainable alternative to conventional agriculture due to its reliance on natural agro-inputs, such as manure based fertilizers and organic pesticides. However, in this analysis we argue that although particular organic farming practices clearly benefit ecosystems and human consumers, the social context in which some organic farms develop, limit the potential environmental benefits of organic agriculture. Specifically, we argue that certified organic farming’s increased reliance on agro-inputs, such as organic fertilizers and pesticides, reduces its ability to decrease global water pollution. We review recent research that demonstrates the environmental consequences of specific organic practices, as well as literature showing that global organic farming is increasing its reliance on agro-inputs, and contend that organic farming has its own metabolic rift with natural water systems similar to conventional agriculture. We use a fixed-effects panel regression model to explore how recent rises in certified organic farmland correlate to water pollution (measured as biochemical oxygen demand). Our findings indicate that increases in the proportion of organic farmland over time increases water pollution. We conclude that this may be a result of organic farms increasing their reliance on non-farm agro-inputs, such as fertilizers.