Previous studies have shown how biogenic silica particles undergo conversion to aluminosilicate phases in large tropical deltaic systems, thus affecting the world ocean budget of major seawater cations. This study tackles the important question of the silica budget in the coastal zone of the Mississippi River Delta, providing evidence for the role of biogenic silica diagenesis in this subtropical system from direct examination of individual diatom particles, sediment leachates and pore-water composition. The estimated reactive silica stored in the study area (5990 km 2) is based on operational leaches that account for altered biogenic silica particles and other authigenic aluminosilicate phases in addition to fresh biogenic silica. Early diagenesis of silica in the delta front occurs mainly where more siliceous material is deposited. An inner-shelf area, where hypoxic conditions are found, significantly contributes to the formation of authigenic products of Si alteration. Data suggest that the limiting factor of silica alteration processes is the availability of detrital phases such as Al and Fe. The estimated total reactive silica accumulation in the study area is 1.45×10 10 mol Si year −1, representing ∼2.2% of the long-term bulk sediment accumulation. On the basis of a conservative appraisal, the authigenic mineral components account for ∼40% of the long-term reactive silica storage. This study shows that non-tropical deltaic systems are significantly more important sinks of silica than previously thought and that, where conditions are favourable, a consistent portion of reactive silica not leaving the shelf is stored within the delta in the form of authigenic components.