Arsenic (As) in the water-soil-rice system has increased globally, threatening global food security. Therefore, the environmental behavior of As in high-arsenic groundwater (GW) for irrigating rice fields needs to be studied urgently. This study aimed to identify the main stage of As absorption by rice and reveal the influence mechanism of As enrichment in the water-soil-rice system with irrigation by high-arsenic GW and the application of soluble organic fertilizers. To this end, pot culture experiments were performed and overlying water, pore water, soil and different part of rice were analyzed. The overlying water and pore water were the HCO
3-Ca type. The chemical properties of the overlying water are mainly related to irrigation water. Irrigation with high-arsenic GW enhanced the reductive dissolution of iron oxides in soil, and increased the As concentration in pore water during the heading stage and filling stage. Irrigation with high-arsenic GW and organic fertilizers can increase the bioavailability of As in soil, which will enhance As enrichment in rice. The accumulation of As in both aboveground and underground parts of rice will increased gradually with the growth of rice. The main period of As uptake by rice roots ranged from the tillering to heading stages, and the transport of As in rice primarily occurred at the grain filling stage. The application of organic fertilizers had little effect on As transport in rice. The high-arsenic GW irrigation will decrease the transport of As from root to straw, and increase the transport of As from straw to grain.