The presence of year-round surface water in streams (i.e., streamflow permanence) is an important factor for identifying aquatic habitat availability, determining the regulatory status of streams, managing land use change, allocating water resources, and designing scientific studies. However, accurate, high resolution, and dynamic prediction of streamflow permanence that accounts for year-to-year variability at a regional extent is a major gap in modeling capability. Herein, we expand and adapt the U.S. Geological Survey (USGS) PRObability of Streamflow PERmanence (PROSPER) model from its original implementation in the Pacific Northwest (PROSPER_PNW) to the upper Missouri River basin (PROSPER_UM), a geographical region that includes mountain and prairie ecosystems of the northern United States. PROSPER_UM is an empirical model used to estimate the probability that a stream channel has year-round flow in response to climatic conditions (monthly and annual) and static physiographic predictor variables of the upstream basin. The structure and approach of PROSPER_UM are generally consistent with the PROSPER_PNW model but include improved spatial resolution (10 m) and a longer modeling period. Average model accuracy was 81 %. Drainage area, upstream proportion as wetlands, and upstream proportion as developed land cover were the most important predictor variables. The PROSPER_UM model identifies decreases in streamflow permanence during climatically drier years, although there is variability in the magnitude across basins highlighting geographically varying sensitivity to drought. Variability in the response of perennial streams to drought conditions among basins in the study area was also observed.