We present a new technique for the estimation of profiles of the rate of dissipation of turbulent kinetic energy ($varepsilon$, TKE) in the marine environment using a standard acoustic Doppler current profiler (ADCP). The technique is based on the structure function method used in radar meteorology. The new method is validated through comparisons of $varepsilon$ estimates from a structure function with simultaneous measurements of profiles of $varepsilon$ made using a freefall profiler, and estimates of the rate of production of TKE using the ADCP variance method. There is a good agreement between the estimates, although some differences in absolute values. A difference in $varepsilon$ estimates between the upstream and downstream beams is attributed to the presence of a significant Reynolds stress.