A continuously operating isothermal dynamic packed-bed reactor was modeled. The model included chemical reaction, gas–liquid mass transfer, convection, axial dispersion, pore diffusion, and catalyst deactivation. The model was solved by using the method of lines. The model was applied on experimental data from citral hydrogenation over a supported nickel catalyst. The experiments had been carried out at 25–65 °C and at 6.1 bar in a laboratory-scale trickle-bed reactor (d = 1 cm; L = 5 cm). The parameters in the model were the rate constants, pore diffusivity, coking rate constant, Peclet number, and gas–liquid mass-transfer coefficient. A sensitivity study was performed to reveal how much a change in each of these changed the product concentration trend. The simulations revealed that the gas–liquid mass-transfer coefficient and effective diffusivity should have been well below expected values to significantly reduce the productivity. The gas–liquid mass transfer and pore diffusion were not rate-limiting; because hydrogen was used in excess, particles were small and the system was dilute. The citral concentration-dependent deactivation model based on site competition was able to describe the observed activity decline. Parameter estimation for the reaction rate and coking rate was carried out. A reasonable agreement with the experimental trends was obtained. An estimate of the Peclet number was obtained from step-response measurements with an inert tracer, which revealed that the reactor did not operate completely as a plug-flow unit. The model described here can be extended to be applicable for other hydrogenation and oxygenation reactions of other fine chemicals.