Tributary confluences are known to affect downstream channel morphology and have the potential to increase downstream habitat heterogeneity. However, few studies have explicitly investigated the effect of tributaries on physical habitat. We used Bayesian modelling to investigate tributary effects on channel morphology, flow velocity, and bed particle size distribution at eight confluences in the Acheron River system in Victoria, Australia, under high-flow and low-flow conditions. Consistent tributary effects across sites and flow stages were a localized increase in channel depth at the confluence and a step increase in channel width in the postconfluence channel. Other tributary effects, such as increased or decreased flow velocity, the presence and placement of confluence bed forms (e.g., scours, pools, bars, and avalanche faces), and altered bed particle size distributions, varied between sites and flow conditions. These results provide evidence of changes to the physical habitat at confluences, which may affect stream biota.