The overuse and misuse of fertilizers have been causing duckweed outbreaks in irrigation ditches and paddy fields in many rice-growing areas. However, how duckweed coverage in a paddy field affects the rice yield and grain quality is under debate because duckweed may act as either a weed, competing with rice for mineral nutrients, or a “nutrient buffer”, providing significant ecological and economic benefits. To understand the effects of duckweed coverage throughout rice growth on the yield and quality of rice grains, an experiment with three Japonica rice cultivars was conducted with fertile lotus-pond bottom soil as a growth medium to provide sufficient mineral nutrients for both the duckweed and rice. Averaged across three rice cultivars, duckweed coverage decreased the panicle density but increased the spikelet density and grain weight, resulting in no significant change in the rice yield. Duckweed coverage had no impact on the processing and appearance quality in general, but significant duckweed-by-cultivar interactions were detected in the head rice percentage and grain chalkiness, indicating different sensitivities of different cultivars in response to the duckweed treatment. The decrease in breakdown and increase in setback values in the rapid visco analyzer (RVA) profile of rice flour suggested that duckweed coverage during rice growth worsened the cooking quality of the rice. However, no significant change in the palatability of the cooked rice was found. The most profound change induced by the duckweed was the nutritional quality; duckweed coverage increased the protein concentration but decreased the concentrations of Mg, Mn, Cu, and Zn in rice grains. This preliminary study suggested that duckweed coverage during rice growth has profound effects on the rice nutrient uptake and grain nutritional quality under the circumstances, and further research on the responses of the rice quality to the duckweed coverage in paddy fields in multiple locations and years is needed.