Currently, a limited number of herbicides is available to treat water-seeded rice in California, with widespread resistance to most of those herbicides. Because no resistant grasses showed resistance to pendimethalin, a series of studies were conducted to evaluate water-seeded rice response to pendimethalin. In a field study conducted at the Rice Experiment Station at Biggs, California, in 2020 and 2021, three pendimethalin formulations, a granule (GR), emulsifiable concentrate (EC), and capsule suspension (CS), were applied at 1.1, 2.3, and 3.4 kg ai ha−1 rates, and at 5, 10, and 15 d after seeding onto water-seeded rice. In addition, a greenhouse study was conducted to examine the response of five common California rice cultivars to GR and CS formulation applications. Echinochloa control levels were reduced at 15 d after seeding after use of EC and CS formulations compared with earlier timings. In both years, rice grain yields were increased by 3,014 kg ha−1 after application of pendimethalin at 3.4 kg ai ha−1 when applied at 15 d after seeding compared with 5 and 10 d after seeding, and similar to 1.1 kg ai ha−1 applications. The GR and CS were safer formulations based on a reduction in injury and an increase in grain yields compared to the EC formulation. Differences in seedling vigor across cultivars appeared to incur an advantage after a pendimethalin application. However, most cultivars evaluated for stand reduction and dry biomass demonstrated tolerance to GR and CS formulation applications only after rice reached the 3-leaf stage. In contrast, an application at 1-leaf stage rice reduced stand up to 68%. Application rate, timing, and formulation are important factors to consider if the use of pendimethalin in water-seeded rice is to be pursued.