The main objective of this study is to predict the performance of an industrial‐scale (ID = 5.8 m) slurry bubble column reactor (SBCR) operating with iron‐based catalyst for Fischer–Tropsch (FT) synthesis, with emphasis on catalyst deactivation. To achieve this objective, a comprehensive reactor model, incorporating the hydrodynamic and mass‐transfer parameters (gas holdup, εG, Sauter‐mean diameter of gas bubbles, d32, and volumetric liquid‐side mass‐transfer coefficients, kLa), and FT as well as water gas shift reaction kinetics, was developed. The hydrodynamic and mass‐transfer parameters for He/N2 gaseous mixtures, as surrogates for H2/CO, were obtained in an actual molten FT reactor wax produced from the same reactor. The data were measured in a pilot‐scale (0.29 m) SBCR under different pressures (4–31 bar), temperatures (380–500 K), superficial gas velocities (0.1–0.3 m/s), and iron‐based catalyst concentrations (0–45 wt %). The data were modeled and predictive correlations were incorporated into the reactor model. The reactor model was then used to study the effects of catalyst concentration and reactor length‐to‐diameter ratio (L/D) on the water partial pressure, which is mainly responsible for iron catalyst deactivation, the H2 and CO conversions and the C5+ product yields. The modeling results of the industrial SBCR investigated in this study showed that (1) the water partial pressure should be maintained under 3 bars to minimize deactivation of the iron‐based catalyst used; (2) the catalyst concentration has much more impact on the gas holdup and reactor performance than the reactor height; and (3) the reactor should be operated in the kinetically controlled regime with an L/D of 4.48 and a catalyst concentration of 22 wt % to maximize C5+ products yield, while minimizing the iron catalyst deactivation. Under such conditions, the H2 and CO conversions were 49.4% and 69.3%, respectively, and the C5+ products yield was 435.6 ton/day. © 2015 American Institute of Chemical Engineers AIChE J, 61: 3838–3857, 2015