The protection of Lake Baikal and the planning of water management measures in the Selenga River Basin require a comprehensive understanding of the current state and functioning of the delta’s ecosystem and hydrogeo- chemical processes. This is particularly relevant in light of recent and expected future changes involving both the hydrology and water quality in the Lake Baikal basin causing spatiotemporal changes in water flow, morphology, and transport of sediments and metals in the Selenga River delta and thus impacting on delta barrier functions. The central part of the delta had been characterized by sediment storage, especially along the main channels, causing a con- tinuous lift of the delta surface by about 0.75 cm/year-1. Theses morphological changes have a significant impact on hydrological conditions, with historical shifts in the bulk discharge from the left to the right parts of the delta which is distinguished by a relatively high density of wetlands. Regions with a high density of wetlands and small channels, in contrast to main channel regions, show a consistent pat- tern of considerable contaminant filtering and removal (be- tween 77 and 99 % for key metals), during both high-flow and low-flow conditions. The removal is associated with a significant concentration increase (2–3 times) of these sub- stances in the bottom sediment. In consequence, geomor- phological processes, which govern the partitioning of flow between different channel systems, may therefore directly govern the barrier function of the delta.