The combination of acoustic Doppler current profilers and the structure
function methodology provide an attractive approach to making extended time
series measurements of oceanic turbulence (the rate of turbulent kinetic energy
dissipation, e) from moorings. However, we show that for deployments
in the upper part of the water column, estimates of e will be biased by the
vertical gradient in wave orbital velocities. To remove this bias, we develop a
modified structure function methodology, which exploits the differing lengthscale dependencies of the contributions to the structure function due to turbulent and wave orbital motions. The success of the modified method is demonstrated through comparison of e estimates based on data from instruments at three depths over a three month period under a wide range of conditions, with appropriate scalings for wind stress and convective forcing.