The presence or absence of a suction condition in an implantable blood pump is determined at least in part based on a parameter related to flow, such as a parameter related to thrust on the rotor of the pump. A local extreme of the parameter representing the minimum flow during ventricular diastole in an earlier interval is used to establish a threshold value. A value of the parameter representing the minimum flow during ventricular diastole in a later interval is compared to this threshold. If the comparison indicates a substantial decline in the minimum flow between the earlier and later intervals is associated with a suction condition. During the absence of a suction condition, the threshold is continually updated, so that the system does not indicate presence of a suction condition if the flow decreases gradually.