Riparian and aquatic vegetation, as well as large wood, are relevant components of river systems. Plants modify (and are affected by) the flow and sediment transport dynamics at a wide range of scales, from the individual plants to the fluvial landscape evolution. This paper aims to review the most recent advances of physical and numerical modelling towards a better understanding, quantification, and prediction of the linkages and feedbacks between water, sediments, vegetation, and wood. Many processes controlling this complex interaction are not yet fully understood. Modelling can be used as a powerful tool that offers the possibility to identify and investigate these processes under controlled conditions. Models are facing the challenge of reproducing a fully coupled bio-geomorphological scenario. This task is complicated by the scarcity of clear mathematical laws linking vegetation and wood dynamics with the common morphological variables, and by the strongly stochastic behaviour of vegetation growth and large wood transport. Several case studies are reported, where living vegetation and transported wood are included into flume scale or numerical models, in order to better assess habitat dynamics, flow characteristics, flood risk, and reach scale morphological evolution.