We propose dynamical models for pulsatile flow and head estimation in an implantable rotary blood pump. Pulsatile flow and head data were obtained using a circulatory mock loop where fluid solutions with different values of viscosities were used as a blood analogue with varying haematocrit (HCT). Noninvasive measurements of power and pump speed were used with HCT values as inputs to the flow model while the estimated flow was used with the speed as inputs to a head estimation model. Linear regression analysis between estimated and measured flows obtained from a mock loop resulted in a highly significant correlation (R² = 0.982) and a mean absolute error (e) of 0.323 L min⁻¹, while for head, R² = 0.933 and e = 7.682 mmHg were obtained. R² = 0.849 and e = 0.584 L min⁻¹ were obtained when the same model derived in the mock loop was used for flow estimation in ex vivo porcine data (N = 6). Furthermore, in the steady state, the solution of the presented flow model can be described by a previously designed and verified static model. The models developed herein will play a vital role in developing a robust control system of the pump flow coping with changing physiological demands.