Provided herein are improved methods for estimating the flow velocity of a fluid in a vessel. Systems and methods are provided herein related to making and/or refining velocity measurements for flowing fluids, both single and multi-phase fluids, in vessels, such as pipes or conduits, utilizing contrast media property agent variations. In one aspect, this disclosure provides a method of determining a flow velocity of a fluid flow in a vessel including: providing a fluid flow having contrast media, the contrast media having a contrast media property variation; providing a detectable signal corresponding to the contrast media property variation; collecting the detectable signal at an upstream receiver to produce a first received signal; collecting the detectable signal at a downstream receiver to produce a second received signal, the downstream receiver being located downstream of the upstream receiver at a distance (L); filtering the first received signal and the second received signal through a contrast media variant filter to produce a first filtered signal and a second filtered signal; cross-correlating the first filtered signal and the second filtered signal to determine a time shift (Δt) between the first filtered signal and the second filtered signal; and estimating the velocity of the fluid flow using this relationship vflow=L/Δt.