The pre-emergent herbicide indaziflam is efficient in the management of weeds in eucalyptus crops, but this plant may develop less in soil contaminated with it. The objective was to evaluate the levels of chlorophylls a and b, the apparent electron transport rate (ETR), growth and dry mass of leaves, stems and roots of Clone I144, in clayey soil, contaminated with the herbicide indaziflam and the leaching potential of this herbicide. The design was completely randomized in a 3 × 5 factorial scheme, with four replications. The leaching of indaziflam in the clayey soil profile (69% clay) was evaluated in a bioassay with Sorghum bicolor, a plant with high sensitivity to this herbicide. The injury and height of this plant were evaluated at 28 days after sowing (DAS). We believe that this is the first work on Eucalyptus in soil with residues of the herbicide indaziflam. Chlorophyll a and b contents and ETR, and height and stem dry mass of Clone I144, were lower in soil contaminated with indaziflam residues. The doses of indaziflam necessary to cause 50% (C50) of injury and the lowest height of sorghum plants were 4.65 and 1.71 g ha−1 and 0.40 and 0.27 g ha−1 in clayey soil and sand, respectively. The sorption ratio (SR) of this herbicide was 10.65 in clayey soil. The herbicide indaziflam leached up to 30 cm depth at doses of 37.5 and 75 g ha−1 and its residue in the soil reduced the levels of chlorophylls a and b, the apparent ETR and the growth of Clone I144.