The wavelet transform (WT) has been successfully implemented in many fields such as signal and image processing, communication theory, optics, numerical analysis, and fluid mechanics. However, the application of WT to describe bedform morphology in coastal areas, oceans, and rivers is rare. The present study demonstrates the capability of WT analysis to fully represent the space-frequency characteristics of signals describing bed topography generated in marine and river environments. In this study WT is used to examine the morphological characteristics of bedforms generated in two separate laboratory facilities: a wave tank and a meandering channel. In the wave tank a set of ripples superimposed upon large wave ripples were generated; while in the meandering channel, 2D and 3D migrating ripples and dunes were observed. The WT proved to be a useful tool in detecting the complex variability of the generated bedform structures. The size distribution of the bottom features such as ripples, large wave ripples and sandbars were first examined along a 2D bed profile. Later analysis studied the variability of features in the transverse direction by using the power Hovmöller. Experiments in the wave tank were conducted for a mobility number of ψ=(10, 28), and a Reynolds wave number of Rew=(17,500, 83,500) which correspond to waves alone (WA) and to combined flow (CF) scenarios, respectively. Experiments in the meandering channel were conducted under a morphological regime that produced mainly migrating sandbars.