Laboratory membrane distillation measurements can be influenced by flow structures generated at the module entrance. Three-dimensional CFD simulations of direct contact membrane distillation examine inlet Reynolds numbers from 10 to 1000, varying side-chamber length and main-channel height. Counter-rotating streamwise vortices form across the geometries studied and persist farther downstream as Reynolds number increases. Geometry changes alter the secondary flow and thermal boundary layer. Relative to a straight-channel baseline, most geometries show stronger temperature polarization at lower Reynolds numbers and weaker polarization at higher Reynolds numbers. Entrance bias thus depends on both geometry and operating condition, rather than a constant correction.