Submarines’ manoeuvrability both in intact and degraded operating conditions is the main design concern starting at the very early stages of design. This increased complexity of the design process compared to a surface vehicle can only be handled by using dynamics numerical simulations on both the vertical and horizontal manoeuvring planes. To this aim, a 6-DoF method is presented, validated, and applied to study the manoeuvring characteristics of several vessels. The analysis has been conducted considering two standpoints, i.e., to verify the design handling capabilities of the vehicles at low and high speeds and to study the off-design residual abilities in the eventual case of emergency operations with jammed/lost-control surfaces. The influence of different design features, such as, e.g., the stern plane “+” and “x” configurations, fairway size and positioning, hull dimensional ratios and restoring capabilities have been analysed in terms of impact on turning ability, course and depth changing abilities, and vertical/horizontal course stability, including the vertical damping ratio and critical velocity.