The operation of any vessel includes risks, such as mechanical failure, collision, property loss, cargo loss, or damage. For modern container ships, safe navigation is challenging as the rate of innovation regarding design, speed profiles, and carrying capacity has experienced exponential growth over the past few years. Prevention of cargo loss in container ship liners is of high importance for the Maritime industry and the waterborne sector as it can lead to potentially disastrous, harmful, or even life-threatening outcomes for the crew, the shipping company, the marine environment, and aqua-culture. With the installment of onboard decision support system(s) (DSS) that will provide the required operational guidance to the vessel’s master, we aim to prevent and overcome such events. This paper explores cargo losses in container ships by employing a novel weather routing optimization DS framework that aims to identify excessive motions and accelerations caused by bad weather at specific times and locations; it also suggests alternative routes and, thus, ultimately prevents cargo loss and damage.