The morphology of the siliceous cell wall (frustule) is fundamental to the identification of diatom species. One of the fundamental questions is the ecophysiological role of the diatom frustule, which often shows morphological plasticity under different growth conditions. In this study, the morphology and elemental composition of the diatom Attheya longicornis were investigated under nutrient-replete (control), iron-depleted and nitrogen-depleted conditions. This cylindrical, unicellular species has four siliceous horns per cell. The horns are each formed from a hoop-like structure with a supporting rod, which greatly increases the surface area (SA) of the cell. Under the iron-depleted conditions, relative to the controls, the SA to cell volume ratio, silicon cell quota and siliceous horn length increased 2.3-, 2.3- and 1.4-fold, respectively. Under the nitrogen-depleted conditions, the cell size decreased without an increase in horn length, and the cellular biogenic silica (BSi) content was the highest between the three growth media. The change in cell geometry and elemental composition modified the sinking behaviour of A. longicornis. Estimated sinking rate was fastest in the nitrogen-depleted cells, followed by the controls and iron-depleted cells. The data suggest that the biogeochemical processes of BSi could show vertically opposite direction depending on the growth-limiting factors through a change in the elemental composition and cell morphology of diatoms. Such plastic responses to nitrogen and iron depletion may contribute to the relatively wide distribution of this species from the coastal to open ocean in the subarctic region.