Raised-field agricultural systems have received attention from scholars involved in the analysis of prehistoric agricultural intensification in the New World. This paper discusses the function of raised fields associated with the Tiwanaku society (500–1100 CE) located on the southern rim of Lake Titicaca in Bolivia. The overnight internal heat storage capacity of Tiwanaku raised-field berms located at the high-altitude (~3810 masl) Bolivian altiplano is analyzed through ANSYS (version 4.2B) finite difference methods to provide an understanding of ancient agricultural engineers’ knowledge regarding how to protect crops from nightly subzero freezing temperatures and water saturation. The present analysis concludes that enhanced berm heat storage capacity derived from solar radiation into multi-layered moist berm agricultural soils, together with radiative heating of berm-surrounding swale water (swale water depth determined from excavation into the groundwater aquifer), was an essential Tiwanaku design element of raised-field agriculture to protect crops from freezing damage during both wet and dry seasons. This paper reports the ANSYS temperature distribution results derived from a raised-field berm swale computer model of ancient excavated raised fields in the form of a 24 h heat input and cooling cycle, which indicates the presence of an internal berm heat storage effect designed to protect crops from freezing damage. The calculations performed use specific hydrological and climatological conditions characteristic of the littoral and near-shore environment of Lake Titicaca. The use of the ANSYS finite element code to investigate the source of internal berm heat storage protecting crops from freezing temperatures, compared to the field test results from experimental use of reconstructed ancient, raised fields, provides an understanding of the technologies developed by Tiwanaku agricultural engineers to increase raised-field agricultural production.