<p>Controlling weeds before their emergence is crucial for minimizing their impacts on crop yield and quality. Bipyridyl herbicides (BPyHs), a class of highly effective and broad-spectrum herbicides, cannot be used as pre-emergence herbicides because they can be absorbed and inactivated by negatively charged soil after application. Here, we design and fabricate an adsorbed-but-active supramolecular pre-emergence herbicide consisting of cationic polyacrylamide and bipyridyl herbicides (CPAM-BPyHs). CPAM is a positively charged polymer. It can preferentially bind to soil particles and shift their electric potential to a more positive value. Thus, it prevents not only runoff but also inactivation of BPyHs. We also develop a BPyHs-resistant rice line by mutation of the gene encoding L-type amino acid transporter 5 (<i>OsLAT5</i>). Field trial results show that the weed control efficiency of CPAM-diquat for direct-seeded herbicide-resistant rice line exceeds 90%. The herbicidal activity can maintain up to one month with only one application. This work offers a method for rice weed control and provides insights into the design of pesticides to prevent soil inactivation and runoff.</p>