Disclosed is a device and a method for measuring stream water depth in real-time through positioning data filtering to ensure the reliability of the measured water depth data even when the stream water depth measurement data is filtered and applied to a small stream having a small basin area and a steep slope. The device for measuring stream water depth in real-time through positioning data filtering includes: a measuring part for measuring the water depth of a stream to be measured; a positioning data filtering part for filtering the water depth data measured by the measuring means by a local linear regression-based bivariate scatterplot smoothing technique through elastic bandwidth application; and a water depth calculating part for calculating a water depth of the stream to be measured by using the positioning data filtered by the positioning data filtering part, and minimizing the uncertainty of the water depth measurement.