The neutron sources at Oak Ridge National Laboratory use a wide suite of sample environment equipment to deliver extreme conditions for a number of experiments. Much of this instrumentation focuses on extremes of temperature, such as cryostats, closed-cycle refrigerators in both low and high temperature configurations, and radiant heating furnaces. When the temperature is controlled across a large range, thermal deflection effects can notably move the sample and affect its alignment in the beam. Here, we combine these sample environments with neutron imaging and machine vision to determine the motion of a representative sample with respect to the neutron beam. We find vertical sample displacement on the order of 1–2 mm and horizontal displacement that varies from near-negligible to 1.2 mm. While these deflections are not relevant for some of the beamlines at the first target station at the spallation neutron source and the high flux isotope reactor, they will become critical for upcoming instrumentation at the second target station, as well as any instruments targeting sub-mm samples, as neutron sources and optics evolve to smaller and more focused beams. We discuss mitigation protocols and potential modifications to the environment to minimize the effect of misalignment due to thermal deflection.