Tracing groundwater flow is of vital importance for managing water resources and understanding the natural water cycle. However, it is a challenge to make accurate measurements of groundwater flow due to its extremely low velocity. A new electromagnetic flowmeter has been developed to conduct non-invasive groundwater flow velocity measurements. In the setup, a customized trapezoidal current source was connected to a 1 m <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\times $ </tex-math></inline-formula> 1 m square coil to generate a strong vertical magnetic field. Two electrodes were used to sense the potential difference caused by water flowing through the magnetic field. A simulation has been developed based on Faraday’s law to evaluate the flow signal under an idealized condition. Two different lab environments have been built for testing the device: an artificial mini-aquifer and a rolling gantry. The measurements show that the flow signal, in practice, generated by the slow-moving water was orders of magnitude smaller than the inductive and capacitive interferences in the system. A linear signal processing model has been developed, allowing the flow signal to be extracted from the measured results. The results show good agreement with simulation and a strong correlation between the flow speed and the processed flow signal, having an <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$R^{2}$ </tex-math></inline-formula> coefficient of 0.94.