This model archive data release includes all models used to characterize the magnitude, spatial distribution and timing of groundwater (GW) flow through lakebed sediments to Upper Klamath Lake (UKL), Oregon, described in the associated journal article (https://doi.org/10.1016/j.scitotenv.2020.142768). One-dimensional vertical models of GW flow (MODFLOW-2005) and solute transport (MT3D-USGS) were calibrated (UCODE) to 2014 observed dissolved silica (Si, 0.2-micron filtered) porewater concentrations in the upper 0.1 m of lakebed sediment to estimate GW flow and Si exchange across the lakebed interface. The Si-based calibrated GW flow rates were then used in conjunction with observed dissolved phosphate-phosphorus (PP) porewater concentrations in the upper 0.1 m of lakebed sediment to estimate the amount of PP reacted during upward flow through the lakebed sediment and the PP discharge to the lake. One-dimensional, vertical GW flow and heat transport models (VS2DH) were calibrated (UCODE) to 2015 and 2017 observed lakebed temperatures to provide estimates of GW-inflow rates at multiple UKL locations. Calibrated GW inflows were greatest in the spring and decreased through the summer. The magnitude and timing of the GW-lake water exchange estimates obtained from these methods were compared to rates obtained from a generalized cross-sectional GW flow model (MODFLOW-NWT) with time-varying recharge. The cross-sectional GW flow model demonstrated that snow-melt GW recharge could be transported rapidly to the lake due to the relatively high permeability and low specific storage of the surrounding volcanic rocks explaining the greater GW discharge to the lake in the spring. This USGS data release contains all the input and output files for the simulations described in the associated journal article (https://doi.org/10.1016/j.scitotenv.2020.142768).