The unlimited nitrogen (N) availability that has characterized crop production in the last few decades is accompanied by environmental burdens, including the greenhouse gas (GHG) emissions associated with fertilizer production, post-application nitrate (NO3-) pollution of water bodies, and emissions of reactive gaseous N forms into the atmosphere. Here, we quantified the environmental tradeoffs of replacing mineral N fertilizer with NO3- and ammonium (NH4+) originating from effluent water of aquaculture in a cucumber (Cucumis sativus) cultivation system. While the yield, nitrogen use efficiency (NUE), and NO3- leaching were similar between the cucumbers fertilized and irrigated (fertigated) by aquaculture effluent water containing 100 mg of NO3--N L-1 (AN), by aquaculture effluent water supplemented with NH4+ (AN+), or by tap water with NO3- and NH4+ added (FN+), there were significant differences in the nitrous oxide (N2O) emissions between the systems. The N2O emissions peaked after each irrigation event followed by an exponential decline. The cumulative N2O emissions were between 60 and 600 g N2O-N ha-1, smaller than predicted based on a fertilizer application rate of 600 kg N ha-1 and were in the order AN+ ≫ FN+ > AN.