Excess nutrient loading to downstream waters has been a persistent environmental concern, especially in agricultural settings. Drainage water management (DWM) is a best management practice intended to reduce nitrogen export from fertilized lands by increasing groundwater levels, slowing the loss of nutrient-rich water and increasing its time in contact with the soil, thus creating greater opportunity for denitrification. This BMP has shown to be effective at reducing dissolved nitrate (TDN) export, but a question remains about potential unintended pollution swapping. The concern is that denitrification could result in nitrous oxide (N2O) emissions and that higher soil moisture could also create suitable conditions for methanogenesis and methane (CH4) emissions. Here we report on two years of monthly static soil gas chamber fluxes and hydrologic nutrient fluxes during a full corn/soybean rotation cycle on the Eastern Shore of Maryland. For N2O, there were significant interactions between season, crop type, and treatment, such as higher fluxes during the fertilization period in the corn year in the DWM treatment, which was consistent with our concern about pollution swapping. However, this brief additional pulse of N2O did not result in a statistically significant increase at an annual scale, nor was there an increase in annual CH4 emissions. At the same time, annual TDN load was significantly lower in the DWM ditches compared to the control. With no significant treatment effect on soil gas fluxes and a significant treatment effect on TDN export, we conclude that pollution swapping of nitrate reduction for greenhouse gases did not occur significantly in this application of DWM to a corn/soybean system. We did, however, find evidence of pollution swapping of phosphorus and nitrogen, as total phosphorus load was higher in the DWM. With more water in the field, the reduced conditions appear to cause a release of soil bound phosphorus. While greenhouse gas production may not be as much of a concern, increased phosphorus export represents a form of pollution swapping that must be accounted for in determining the value of this BMP.