Waterlogging is one of the major abiotic stresses limiting tomato (Lycopersicum esculentum Mill.) productivity on tropical wetland areas in Indonesia, including East Kalimantan, which has high rainfall. This study aimed to determine the effects of waterlogging level and variety on the growth, yield, and root anatomical structure of four tomato varieties (Servo, Tora IPB, Timoty, and Royal 58). The study was conducted in Rempanga Village, Loa Kulu District, Kutai Kartanegara Regency, East Kalimantan, using a Split Plot design with the water-table depth below the growing medium surface as the main plot (no waterlogging/h0; 30 cm below the medium/h1; 20 cm below the medium/h2; and 10 cm below the medium/h3, kept constant from transplanting to harvest) and variety as the subplot, each with three replications. Data were analysed using analysis of variance followed by Duncan's Multiple Range Test (DMRT) at the 5% level. The results showed that h1 produced the best growth and yield response compared with the other treatments, with the highest leaf number, plant height, stem diameter, root length, and root weight, and productivity reaching 1438.76 g/polybag, whereas the deepest waterlogging (h3) suppressed all parameters, resulting in the lowest productivity (60.73 g/polybag). The Royal 58 variety showed the best tolerance, characterised by the highest root dry weight and productivity among the four varieties tested. Root anatomical observation on Royal 58 indicated cell wall thickening and a porous cortical structure resembling aerenchyma tissue under h1, a pattern also consistently observed in the other three varieties. This study provides baseline information for developing waterlogging-tolerant tomato cultivation on suboptimal land in Indonesia.