Measurements of spatial and temporal changes in the grain size distribution are crucial to improving the modelling of sediment transport and associated grain size-selective processes. We present three complementary techniques to determine such variations in the grain size distribution in sand-gravel laboratory experiments, as well as the resulting stratigraphy: (1) particle colouring, (2) removal of sediment layers, and (3) image analysis. The resulting stratigraphy measurement method has been evaluated in two sets of experiments. In both sets three grain size fractions within the range of coarse sand to fine gravel were painted in different colours. Sediment layers are removed using a wet vacuum cleaner. Subsequently areal images are taken of the surface of each layer. The areal fraction content, i.e. the relative presence of each size fraction over the bed surface, is determined using a colour segmentation algorithm which provides the areal fraction content of a specific colour (i.e., grain size) covering the bed surface. Particle colouring is not only beneficial to this type of image analysis but also observing and understanding grain size-selective processes. The stratigraphy based on areal fractions is measured with sufficient accuracy. Other advantages of the proposed stratigraphy measurement technique are: (a) rapid collection and processing of a large amount of data, (b) very high spatial density of information on the grain size distribution (so far unequalled in other methods), (c) the lack of disturbances to the bed surface, (d) only minor disturbances to the substrate due to the removal of sediment layers, and (e) the possibility to return a sediment layer at its original elevation and continue the flume experiment. The areal fractions can be converted into volumetric fractions using a conversion model. The proposed empirical conversion model is based on a comparison between the photogrammetry results and dry sieve analysis.