The temporal alteration of the hydrodynamic regime in rivers due to navigation has significant effects on riverine ecosystems. Most of the key mechanisms and interactions between hydrodynamic and ecological variables have already been revealed; however, the quantitative evaluation of biotic and abiotic variables still stands a challenge. This paper aims to present a thorough, spatiotemporal framework, involving field and computational tools, for the assessment of wave hydrodynamics in the littoral zone of rivers, where its ecological relevance is the most significant. The temporal variation of significant wave heights is derived from high-frequency pressure measurements, offering a well-comparable statistical evaluation of individual wave events considering the duration of different wave intensities. Acoustic Doppler velocimetry (ADV) is used for the assessment of near-bank velocities, from which the secondary wave-related components have been filtered offering relevant validation data for numerical modelling. The small footprint of the ADVs is extended with up-to-date computational fluid dynamics modelling. Wave spectra derived from the pressure measurements are used as boundary conditions for phase-resolved irregular wave modelling with the level set method based numerical model REEF3D. The properly validated model offers the assessment of the most relevant hydrodynamic variables (e.g., velocity or turbulent kinetic energy) in a spatially extended manner, from which the hydrodynamic footprint of the wave events can be interpreted in a statistical fashion. The implementation of the proposed framework is illustrated through a case study at a Hungarian section of the Danube River.