A morphological filter (MF) is presented for the determination of beat-to-beat mean rotary left ventricular assist device (LVAD) flow rate, measured using an implanted flow probe. The performance of this non-linear filter was assessed using LVAD flow rate (QLVAD) data sets obtained from in silico and in vivo sources. The MF was compared with a third-order Butterworth filter (BWF) and a 10-s moving average filter (MAF). Performance was assessed by calculating the response time and steady state error across a range of heart rates and levels of noise. The response time of the MF was 3.5 times faster than the MAF, 0.5 s slower than the BWF, and had a steady state error of 2.61 %. It completely removed pulsatile signal components caused by residual ventricular function, and tracked sharp transient changes in QLVAD better than the BWF. The use of a two-stage MF improved the noise immunity compared to the single-stage MF. This study showed that the good performance characteristics of the non-linear MF make it a more suitable candidate for embedded real-time processing of QLVAD than linear filters.