Excess nitrogen resulting from agricultural fertilizer and manure applications on the Eastern Shore degrades the Chesapeake Bay's water quality and causes environmental issues such as algal blooms and "dead zones". Drainage water management (DWM) is an effective best management practice (BMP) to reduce hydrological nitrate export from croplands to surface and ground water by controlling the timing and the amount of ditch discharge and retaining water within ditches and adjacent fields using drainage control structures (DCS). While promoted denitrification in the subsurface and reduction in nitrate leaching are intended consequences of maintaining higher water table level, an unintended environmental consequence is possible production of nitrous oxide (N2O) from denitrification and methane (CH4) from methanogenesis, which are both potent greenhouse gases (GHGs). Whether the application of DWM leads to a "pollution swapping" concern (i.e., trading reduction of nitrate concentrations in ditch water for increases in emissions of N2O and CH4 to the atmosphere) is a question that must be addressed before more widespread implementation of DWM can be endorsed. In this dissertation, I employed a micrometeorological method called the flux gradient (FG) method to a corn-soybean rotation agricultural system with DCS in eastern Maryland on the Delmarva Peninsula to answer this question. This method was chosen because it allows near-continuous measurements of soil trace gas exchanges at multiple locations with a single laser spectrometer at a fine temporal resolution without disturbing the microclimate between soils and the atmosphere. Soil N2O and CH4 fluxes were quantified using the FG method on this drainage water managed farm for three consecutive years when no fertilizer, synthetic fertilizer, and biosolids were applied in 2018 (soybean), 2019 (corn), and 2020 (corn), respectively. Statistical tests indicated that there were no consistent treatment effects of DWM on soil GHG emissions between DWM and non-DWM conditions, suggesting that DWM did not trade the intended consequence of reduced nitrate leaching for the unintended consequence of increased soil GHG emissions. The biosolid addition in 2020 led to the largest N2O emissions among the three years, while the lowest N2O emissions in the growing season were found in the unfertilized soybean year of 2018. In contrast, different fertilization regimes did not yield distinct differences between the three years for CH4 fluxes. In addition, some potential methodological concerns associated with this tower-based micrometeorological approach were addressed and resolved, conferring confidence that the FG method can be applied simultaneously to multiple plots for N2O and CH4 measurements. This research adds to the existing understanding of the impacts of DWM on soil GHG emissions and suggests that this BMP could be applicable in other regions of the Chesapeake Bay as well as other watersheds. This work also contributes to the efforts of studying the impacts of soil organic amendments on soil GHG emissions and deriving improved estimates of emission factors (EFs) for organic amendments.