Urban heat is one of the world’s most significant climate hazards for vulnerable communities. It is especially hazardous for poor, elderly, and otherwise overburdened members of society causing increasingly more deaths each year among these urban constituents. With each new heatwave, heterogeneous heat exposure, both indoor and outdoor, across urban neighborhoods becomes more apparent. Understanding how neighborhood geometry, or morphology, amplifies or mitigates extreme heat within specific neighborhoods is critical to improving urban resilience to future heat extremes. We show that differences in meteorological output from the Weather Research and Forecasting (WRF) model run at 270m horizontal resolution using 10m, 100m and 1km resolution 3D neighborhood morphological inputs and with no morphological inputs produce different spatial variability in temperature, humidity, and other meteorological variables across a city. Especially large differences are evident between simulations run without 3D morphological input and those run with some type of 3D morphology. These findings suggest that understanding neighborhood level urban sustainability under extreme heat waves, especially for vulnerable neighborhoods, requires explicit representation of the built environment in numerical weather models.