Sexual reproduction of an amphibious macrophyte Schoenoplectus lineolatus (Fr. et Stav.) T. Koyama (Cyperaceae) was observed in three irrigation ponds with different water regimes in Hyogo Prefecture, western Japan. In each pond, inflorescence formation, flowering (anthesis), and seed set were recorded at three water depths (shallow, middle, and deep). Inflorescence formation was observed under submerged conditions in the three ponds. In Oku-ike Pond, anthesis was observed when the water level dropped in August and early September. Flowers opened after the emergence of the inflorescence into the air. In contrast, anthesis did not occur, despite inflorescence formation, in the other two ponds with no water level drop or a short period of water level drop. Submerged inflorescences could not set seeds unless pollination had already occurred in the air. Finally, inflorescence formation under submerged conditions was considered to be a waiting strategy for water drawdown in the irrigation ponds where marked water level decreases occur from summer to autumn. Anthesis can quickly start soon after the emergence of inflorescences.