Fresh market pepper and tomato are important crops in Florida. Production primarily occurs on raised beds covered with plastic mulch. Weeds emerging between the rows are often controlled with multiple applications of burndown and soil-residual herbicides. Crop damage attributed to root uptake of herbicides applied between the rows has been reported. An experiment was conducted in a greenhouse at the Gulf Coast Research and Education Center to examine the effect of root uptake of paraquat and paraquat tank-mixed with flumioxazin on pepper and tomato growth and yield. Herbicides were applied via subsurface irrigation at 0.0625×, 0.125×, 0.25×, 0.5×, 1×, 2×, 4×, 8×, and 16× labeled rates. The 1× rate was based on the estimated label rate that would be applied per plant in the field and was 0.122 g ai plant−1 (1,542 g ai ha−1) and 0.011 g ai plant−1 (143 g ai ha−1) for paraquat and flumioxazin, respectively. Root uptake caused necrosis of the veins, followed by complete tissue death at higher rates. The percentage of crop damage increased with herbicide rate for both species (P < 0.0001), with greater damage observed at the lower rates with the tank mix than with the paraquat alone. A reduction in shoot biomass and fruit yield of both crops was observed following root uptake. These results suggest that uptake of paraquat or paraquat tank-mixed with flumioxazin by pepper and tomato roots in a field situation is possible.