Microswimmers are sub-millimeter swimming robots that show potential as a platform for controllable locomotion in applications, including targeted cargo delivery and minimally invasive surgery. To be viable for these target applications, microswimmers will eventually need to be able to navigate environments with dynamic fluid flows and forces. Experimental studies with microswimmers towards this goal are currently rare because of the difficulty of isolating intentional microswimmer locomotion from environment-induced motion. In this work, we present a method for measuring microswimmer locomotion within a complex flow environment using fiducial microspheres. By tracking the particle motion of ferromagnetic and non-magnetic polystyrene fiducial microspheres, we capture the effect of fluid flow and magnetic field gradients on microswimmer trajectories. We then determine the field-driven translation of these microswimmers relative to fluid flow and demonstrate the effectiveness of this method by illustrating the motion of multiple microswimmers through different flows.