This study investigates the physical processes that control riparian tree seed dispersal and germination within a Mediterranean climate. During the dispersal stage, riparian species are described by advective-dispersion flow to transport seeds while transient storage processes deposit seeds along the bank margin. Seeds remain dormant until appropriate environmental conditions initiate germination. The research is based on a two-part study that presents a one-dimensional, numerical dispersal model and a hydrothermal time germination model coupled with historic flow conditions. The models were applied to the white alder (Alnus rhombifolia) seed population in Northern California, USA. The dispersal model highlights the importance of geomorphological features and flow structures to transport and preferentially deposit seeds. The germination model determines the average time to germinate during the dispersal period while stage height conditions provide insights into the initial recruitment stages of a species community structure.