The need for characterizing turbulence in the ocean recently led to new techniques, among which is the use of acoustic Doppler current profilers (ADCP) on various stationary and moving platforms. This study aims to estimate the dissipation of turbulent kinetic energy, ", and the advective oceanic velocities from two 1.2-MHz single ping mode ADCPs mounted on a remotely operated towed vehicle (ROTV). The data consist of an equatorial transect of the Atlantic Ocean on which the ROTV was undulating between the surface and 300 meters depth. " is then estimated from the second and third order structure functions. This work outlines the development and the results of the application of this method on the available dataset. The conclusion is that for this data set, the signal to noise ratio is too low. We recommend acquiring at least an order of magnitude more individual raw pings. This would more likely let the statistics coverage to a reliable estimate of ". Additionally, prior knowledge of the Ozmidov scale, i.e. the size of the largest overturning eddies, is helping to ensure that roughly ten bins are within the inertial subrange. This approach enables continuous measurements of proles for a whole transect, as well as measurements close to the surface by operating the ROTV outside the vessel-induced turbulence zone. This new technique has the advantage to broaden the measurement range of high-frequency ADCP measurements by the undulation of the vehicle.