The Elkhorn and Loup Rivers in Nebraska provide water for irrigation, recreation, hydropower production, aquatic life, and municipal water systems for the Omaha and Lincoln metropolitan areas. Groundwater is another important resource in the region and is extracted primarily for agricultural irrigation. Water managers of the area are interested in balancing and sustaining the long-term uses of these essential surface-water and groundwater resources. Thus, a cooperative study was established in 2006 to compile reliable data describing hydrogeologic properties and water-budget components and to improve the understanding of stream-aquifer interactions in the Elkhorn and Loup River Basins. A groundwater-flow model was constructed as part of the first two phases of that study as a tool for understanding the effect of groundwater pumpage on stream base flow and the effects of management strategies on hydrologically connected groundwater and surface-water supplies. The third phase of the study was implemented to gain additional geologic knowledge and update the ELM with enhanced water-budget information and refined discretization of the model grid and stress periods. As part of that effort, the ELM is being reconstructed to include two vertical model layers, whereas phase-one and phase-two simulations represented the aquifer system using one vertical model layer. This report presents a map of and methods for developing the elevation of the base of the upper model layer for the phase-three ELM. Digital geospatial data of elevation contours and geologic log sites used to estimate elevation contours are available as part of this report.