The ANTARES neutrino telescope is the largest and longest-operated underwater neutrino telescope. Data acquisition conditions in a marine environment are not stable in time: biological and physical phenomena follow a seasonal evolution producing a periodical change of the rates registered at the neutrino telescope. Variations in the sea current velocity also affect the measured baseline value and the burst fraction on short time scales. Monte Carlo simulations of the detector response to charged particles in the proximity of the telescope should reproduce the conditions of the medium and of the acquisition setup as much as possible. An efficient way to account for their variability is to extract related information directly from the data runs. A Run-by-Run simulation procedure has been developed to follow the time evolution of data acquisition in ANTARES.