To explore links between glacier dynamics, sediment yields and the accumulation of glacial sediments in a temperate setting, we use extensive glaciological observations for Columbia Glacier, Alaska, and new oceanographic data from the fjord exposed during its retreat. High-resolution seismic data indicate that 3.2 × 108 m3 of sediment has accumulated in Columbia Fjord over the past three decades, which corresponds to ~5 mm a−1 of erosion averaged over the glaciated area. We develop a general model to infer the sediment-flux history from the glacier that is compatible with the observed retreat history, and the thickness and architecture of the fjord sediment deposits. Results reveal a fivefold increase in sediment flux from 1997 to 2000, which is not correlated with concurrent changes in ice flux or retreat rate. We suggest the flux increase resulted from an increase in the sediment transport capacity of the subglacial hydraulic system due to the retreat-related steepening of the glacier surface over a known subglacial deep basin. Because variations in subglacial sediment storage can impact glacial sediment flux, in addition to changes in climate, erosion rate and glacier dynamics, the interpretation of climatic changes based on the sediment record is more complex than generally assumed.