Water is one of the main dispersal agents of plant seeds and influences plant population dynamics and community structure. Although a large proportion of paddy fields are subjected to irrigation, limited research has addressed weed seed dispersal via water in rice-based systems. In this study, safranin T-dyed Beckmannia syzigachne seeds were released and their movement was tracked to characterize their dispersal dynamics via water in an irrigation canal and in a rice field. B. syzigachne seeds, floating on the water surface, moved from their release point at the canal entrance via irrigation water along the irrigation canal. A well-simulated Gaussian plume model indicated that the seed dispersal of B. syzigachne conformed to a leptokurtic distribution, and the peak dispersal kernel showed that seeds moved along the irrigation water flow to approximately 800–1000 m away from the release point 36 h after release into the canal. When seeds were released in the center of a flooded field, a total of 60% of the released seeds were water-dispersed to the northwest corner by the southeast prevailing monsoon wind within 72 h. The well-fitted Gauss 2D-model illustrated the widening of the seed distribution range with time and dispersal pattern with an accumulation center in the field. Our study is the first to show that buoyant weed seeds are mainly dispersed by irrigation water in both the canal and field and that the water dispersal of seeds influences the spatial deposition and distribution of the weed seed bank and strongly affects weed occurrence patterns in irrigated fields.