Depressional wetlands of the extensive U.S. and Canadian Prairie Pothole Region afford numerous ecosystem processes that maintain healthy watershed functioning. However, these wetlands have been lost at a prodigious rate over past decades due to drainage for development, climate effects, and other causes. Options for management entities to protect the existing wetlands, and their functions, may focus on conserving wetlands based on spatial location vis-à-vis a floodplain or on size limitations (e.g., permitting smaller wetlands to be destroyed but not larger wetlands). Yet the effects of such management practices and the concomitant loss of depressional wetlands on watershed-scale hydrological, biogeochemical, and ecological functions are largely unknown. Using a hydrological model, we analyzed how different loss scenarios by wetland size and proximal location to the stream network affected watershed storage (i.e., inundation patterns and residence times), connectivity (i.e., streamflow contributing areas), and export (i.e., streamflow) in a large watershed in the Prairie Pothole Region of North Dakota, USA. Depressional wetlands store consequential amounts of precipitation and snowmelt. The loss of smaller depressional wetlands (<3.0ha) substantially decreased landscape-scale inundation heterogeneity, total inundated area, and hydrological residence times. Larger wetlands act as hydrologic "gatekeepers," preventing surface runoff from reaching the stream network, and their modeled loss had a greater effect on streamflow due to changes in watershed connectivity and storage characteristics of larger wetlands. The wetland management scenario based on stream proximity (i.e., protecting wetlands 30 m and ~450 m from the stream) alone resulted in considerable landscape heterogeneity loss and decreased inundated area and residence times. With more snowmelt and precipitation available for runoff with wetland losses, contributing area increased across all loss scenarios. We additionally found that depressional wetlands attenuated peak flows; the probability of increased downstream flooding from wetland loss was also consistent across all loss scenarios. It is evident from this study that optimizing wetland management for one end goal (e.g., protection of large depressional wetlands for flood attenuation) over another (e.g., protecting of small depressional wetlands for biodiversity) may come at a cost for overall watershed hydrological, biogeochemical, and ecological resilience, functioning, and integrity.