The authors show that vertical turbulent fluxes in the upper ocean can be measured directly with an autonomous underwater vehicle (AUV). A horizontal profile of vertical water velocity is obtained by applying a Kalman smoother to AUV motion data. The smoother uses a linearized model for vehicle motion and vehicle data such as depth, pitch, and pitch rate to produce an optimal estimate of the state of the system, which includes other vehicle variables and the vertical water velocity. Vertical water velocity estimated by applying the smoother to data from the autonomous microconductivity temperature vehicle (AMTV) is accurate at horizontal scales from three to several hundred meters, encompassing the energy-containing scales of most oceanic turbulence. The zero-lag covariances between vertical water velocity and concurrent measurements of temperature or salinity represent the heat and salt fluxes, respectively. The authors have measured horizontal profiles of turbulent fluxes with two different AUVs in three separate polar ocean experiments using this technique. Flux magnitudes and directions are reasonable and in general agreement with fixed turbulence sensors. With this technique, one can gather boundary layer data in inaccessible regions without disturbing or affecting the surface.