Atomistic simulations of carbon nanotubes (CNTs) in a liquid environment are performed to better understand thermal transport in CNT-based nanofluids. Thermal conductivity is studied using nonequilibrium molecular dynamics (MD) methods to understand the effective conductivity of a solvated CNT combined with a novel application of Hamilton–Crosser (HC) theory to estimate the conductivity of a fluid suspension of CNTs. Simulation results show how the presence of the fluid affects the CNTs ability to transport heat by disrupting the low-frequency acoustic phonons of the CNT. A spatially dependent use of the Irving–Kirkwood relations reveals the localized heat flux, illuminating the heat transfer pathways in the composite material. Model results can be consistently incorporated into HC theory by considering ensembles of CNTs and their surrounding fluid as being present in the liquid. The simulation-informed theory is shown to be consistent with existing experimental results.