This paper examines near-bottom shear stresses at two locations in a small, highly stratified estuary: the Navesink River, New Jersey, USA. The shear stresses obtained from acoustic Doppler current profilers (ADCPs) operating in the recently developed mode 11 at a high spatial resolution are examined in detail. Measurement noise of the ADCP is estimated using autocorrelation analyses and is found to be small but correlated with velocity. Measurement noise in estimates of Reynolds stress is found to be somewhat smaller than that obtained in earlier studies for the ADCP operating in mode 4. Internal waves may have produced observed correlated oscillatory motions. The effect of these motions on Reynolds stress estimates is quantified and shown to be at least an order of magnitude less than the total measured stress and probably much less. The high-spatial-resolution profiles from the ADCP operating in mode 11 allow excellent measurements of near-bed vertical velocity gradients. Log profile estimates of stress are poorly related to Reynolds estimates, even when stability measures based on near-bed density gradients are taken into account. We show that upper layer pycnoclines likely inhibit turbulence and bias log profile estimates even at a half meter above the bed, where the water column is well mixed.