AbstractThe Holocene stratigraphy of Sylhet basin, a tectonically influenced sub‐basin within the Ganges‐Brahmaputra‐Meghna delta (GMBD), provides evidence for autogenic and allogenic controls on fluvial system behaviour. Using Holocene lithology and stratigraphic architecture from a dense borehole network, patterns of bypass‐dominated and extraction‐enhanced modes of sediment transport and deposition have been reconstructed. During a ~3‐kyr mid‐Holocene occupation of Sylhet basin by the Brahmaputra River, water and sediment were initially (~7.5–6.0 ka) routed along the basin's western margin, where limited downstream facies changes reflect minimal mass extraction and bypass‐dominated transport to the basin outlet. Sediment‐dispersal patterns became increasingly depositional ~6.0–5.5 ka with the activation of a large (~2250 km2) splay that prograded towards the basin centre while maintaining continued bypass along the western pathway. Beginning ~5.0 ka, a second splay system constructed an even larger (~3800 km2) lobe into the most distal portions of the basin along the Shillong foredeep. This evolution from a bypass‐dominated system to one of enhanced mass extraction is well reflected in (i) the rapid downstream fining of deposited sand and (ii) a change in facies from amalgamated channel deposits to mixed sands and muds within discrete depositional lobes. The persistence of sediment bypass suggests that seasonal flooding of the basin by local runoff exerts a hydrologic barrier to overbank flow and is thus a principal control on river path selection. This control is evidenced by (i) repeated, long‐term preference for occupying a course along the basin margin rather than a steeper path to the basin centre and (ii) the persistence of an under‐filled, topographically low basin despite sediment load sufficient to fill the basin within a few hundred years. The progradation of two 10–20‐m thick, sandy mega‐splays into the basin interior reflects an alternative mode of sediment dispersal that appears to have operated only in the mid‐Holocene (~6.0–4.0 ka) during a regional weakening of the summer monsoon. The reduced water budget at that time would have lowered seasonal water levels in the basin, temporarily lessening the hydrologic barrier effect and facilitating splay development into the basin interior. Overall, these results place basin hydrology as a first‐order control on fluvial system behaviour, strongly modifying the perceived dominance of tectonic subsidence. Such coupling of subsidence, fluvial dynamics and local hydrology have been explored through tank experiments and modelling; this field study demonstrates that complex, emergent behaviours can also scale to the world's largest fluvial system.