Magnetic shape memory (MSM) alloy micropumps outperform traditional technology through a combination of high pumping precision (below 100 nl per gulp), high controllability and repeatability, high pumping pressure (10 bar), and small size. The pumping method utilizes no moving parts; instead, the material acts as a muscle, replacing valves and mechanical components with a single material that shape changes to move fluid in a peristaltic manner. We present measurement and analysis of the cyclical variability of MSM pump flow as measured with an inline flow sensor. We correlate this flow to the local fluctuations of the MSM surface profile as measured by a laser displacement sensor. These two measurement techniques elucidate the deformation mode the MSM pump experiences during operation, allowing designers of MSM pumps to better accommodate and manipulate material behaviour.