Recent revisions to the definition of the “waters of the United States” (WOTUS) have considerably altered how wetlands are federally regulated under the Clean Water Act. The two most recent modifications to WOTUS, the Clean Water Rule (CWR) and the Navigable Waters Protection Rule (NWPR), represent two opposing approaches to the federal wetland policy. Despite their implementation, the impacts of these rules on the regulation of wetlands have as of yet been poorly characterized at broad spatial scales. Using New York State (NYS) as a case study, we evaluated the jurisdictional statuses of more than 373,000 wetlands under the CWR and the NWPR to assess the landscape-scale effects of WOTUS re-definitions. We found that statewide and within each of NYS’s hydrologic regions, the NWPR protects fewer wetlands and less total wetland area than the CWR. The efficacy of the two regulations varied considerably in space across NYS, highlighting the need for comprehensive, nationwide assessments of wetland policy outcomes. We also observed that both rules produced non-uniform patterns in jurisdiction across a range of landscape positions and wetland sizes, preferentially protecting large wetlands close to the stream network. This effect was particularly pronounced under the NWPR, which excludes all geographically isolated wetlands from protection. Our findings in NYS emphasize the existence of unique patterns in protected wetlands across spatial scales, highlighting the value in applying geospatial analyses to evaluate environmental policy.