In regions of sugar beet cultivation, weed beet infestations are responsible for economic losses. Weed beet belongs to the same species as the cropped plant, thus rendering herbicide control impossible in conventional sugar beet where costly practices such as manual weeding of bolters must be carried out instead. Genetically-modified herbicide-tolerant (GMHT) sugar beet varieties might provide an alternative in fields heavily infested with weed beet. However, accidental bolting of GMHT plants would result in pollen-mediated transgene flow towards weed beets. The objective of the present paper was to use a spatiotemporal simulation model for comparing three production systems with different cultural practices to evaluate the risk of herbicide-tolerant weed beet populations in a small agricultural region where GMHT and conventional sugar beet coexist. The GENESYS-Beet simulation model was used in a case study of a French sugar beet production region where three types of intensive production systems had been identified: (1) “potato grower”; (2) “beet grower”; and (3) “cereal grower”. The three production systems were successively simulated on a real 149 field map extracted from the studied region. Our simulation results show that gene flow is inevitable, both in time and in space, but that it varies considerably with the cropping system. Similar results were obtained for oilseed rape. Simulation models proved to be powerful tools for predicting the effect of alternative methods on gene flow to and from weed populations. However proposals still require economic feasibility studies.