A noninvasive approach to the task of pulsatile flow estimation in an implantable rotary blood pump (iRBP) has been proposed. Employing six fluid solutions representing a range of viscosities equivalent to 20-50% blood hematocrit (HCT), pulsatile flow data was acquired from an in vitro mock circulatory loop. The entire operating range of the pump was examined, including flows from -2 to 12 L/min. Taking the pump feedback signals of speed and power, together with the HCT level, as input parameters, several flow estimate models were developed via system identification methods. Three autoregressive with exogenous input (ARX) model structures were evaluated: structures I and II used the input parameters directly; structure II incorporated additional terms for HCT; and the third structure employed as input a non-pulsatile flow estimate equation. Optimal model orders were determined, and the associated models yielded minimum mean flow errors of 5.49% and 0.258 L/min for structure II, and 5.77% and 0.270 L/min for structure III, when validated on unseen data. The models developed in this study present a practical method of accurately estimating iRBP flow in a pulsatile environment.