The offshore industry is adopting Autonomous Underwater Vehicles (AUVs), to decrease the costs associated with surveying underwater sites. Despite requiring less human supervision, AUVs still depend on costly servicing from a vessel, before and after deployment. Combining an AUV with an Unmanned Surface Vessel (USV), a survey vessel that operates without humans on board, could drastically reduce operational costs. This thesis focuses on the crucial requirement of this combination: the autonomous docking of the AUV to the USV. Current studies focused on the AUV-USV combination lack effective solutions for docking in rough ocean conditions, while this is key for its operational employability. These studies have explored horizontal docking approaches, while an unexplored alternative is a vertical docking approach from below the USV. This approach may experience reduced influence of waves, as the wave disturbance acting on the AUV and the USV are phase synchronized. The objective of this study is to evaluate the viability of vertically docking an AUV to a USV in rough seas, using the Lobster Scout AUV as a case study for an initial performance evaluation. This study first identified and scoped the key elements for this initial performance evaluation, which included the waves, the USV, the Lobster Scout, the Docking Station (DS), and vertical docking Guidance Navigation and Control (GNC). Furthermore, the scope was limited to the critical docking stage, where the vehicles are within meters of each other. The study used simulation as the primary method to investigate the thesis objective and a 2-Dimensional (2D) model was developed to simulate the system dynamics, which was fitted and verified using a variety of methods, including analytical calculations, mesh convergence studies, experiments, and visual analysis. To determine the viability of the vertical docking approach of the USV-AUV combination, a probability distribution-based method was developed. Viability was expressed in terms of the maximum operational sea state and the estimated operational up-time. Since docking success under the presence of waves is described probabilistically, the requirement was set that at least 991 out of a 1000 docks should be successful. Furthermore, Monte Carlo simulations were used to obtain the docking performance over a variety of sea states, navigational settings, and different guidance and control methods. A target state vertical guidance method using way-points was designed with various Proportional-Integral-Derivative (PID) based controllers to guide the Lobster Scout to the DS. It was also determined whether kinematic prediction or polynomial prediction could improve docking performance and the impact of navigation on docking performance was investigated. It was found that the vertical docking approach shows promise for enabling a reliable AUV-USV combination for the Lobster Scout in medium to rough seas, with a significant wave height of 1.65 m and 3.6 m respectively, resulting in an estimated annual operational up-time of 59 % to 94 % in the North Sea. Furthermore, there is potential to achieve even higher sea states with improved GNC methods. Overall, this study suggests that the vertical docking approach can lead to a viable AUV-USV combination with improved operational employability compared to current docking studies using horizontal approaches, although the author is of the opinion that both approaches require further investigation.