With the constantly increasing pressure of the competitive environment, supply chain (SC) decision makers are forced to consider several aspects of business climate. More specifically, they should take into account the endogenous features (e.g., available means of transportation, and the variety of products) and exogenous criteria (e.g., the environmental uncertainty, and transportation system conditions). In this paper, a mixed integer nonlinear programming (MINLP) model for dynamic design of a supply chain network is proposed. In this model, multiple products and multiple transportation modes, the time value of money, traffic congestion, and both supply-side and demand-side uncertainties are considered. Due to the complexity of such models, conventional solution methods are not applicable; therefore, two hybrid Electromagnetism-Like Algorithms (EMA) are designed and discussed for tackling the problem. The numerical results show the applicability of the proposed model and the capabilities of the solution approaches to the MINLP problem.