Tidal energy resource characterisation using acoustic velocimetry sensors mounted on the seabed informs developers of the location and performance of a tidal energy converter (TEC). This work studies the consequences of miscalculating the established flow direction, i.e., the direction of assumed maximum energy yield. Considering data only above the proposed TEC cut-in velocities showed a difference in the estimated flow direction of up to 4°. Using a power weighted rotor average (PWRA) method to obtain the established flow direction resulted in a difference of less than 1° compared with the hub-height estimate. This study then analysed the impact of turbine alignment on annual energy production (AEP) estimates for a non-yawing tidal turbine. Three variants of horizontal axis tidal turbines, which operate in different locations of the water column, were examined; one using measured data, and the other two via modelled through power curves. During perfect alignment to the established flow direction, natural variations in flow meant that the estimate of AEP differed by up to 1.1% from the theoretical maximum of a fully yawed turbine. In the case of misalignment from the established flow direction, the difference in AEP increased. For a 15° misalignment, the AEP differed by up to 13%. These results quantify important uncertainties in tidal energy site design and performance assessment.