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Regional seas are of paramount importance for human life. They play a key role in the planetary Earth system dynamics while they also represent a fundamental component of the global economy, making the overuse of ocean resources and the consequent degradation of local marine ecosystems a major concern of our society. Regional ocean modelling represents a powerful and efficacious tools to understand, manage and preserve the changing oceans and seas. This PhD research focuses on improving some of the techniques used for the numerical modelling of regional seas. This is done by developing a novel vertical discretisation scheme for numerical ocean modelling and conducting numerical experiments in an idealized domain as well as in two complex and contrasting real marine environments, the Black Sea and the Dead Sea. In Chapter 3 a Multi-Envelope generalised coordinate system for numerical ocean modelling is introduced. In this system, computational levels are curved and adjusted to multiple `virtual bottoms' (aka envelopes) rather than following geopotential levels or the actual bathymetry. This allows defining computational levels which are optimised to best represent different physical processes in different sub-domains of the model. In particular, we show how it can be used to improve the representation of tracer advection in the ocean interior. The new vertical system is compared with a widely used z-partial step scheme. The modelling skill of the models is assessed by comparison with the analytical solutions or results produced by a model with a very high resolution z-level grid. Three idealised process-oriented numerical experiments are carried out. Experiments show that numerical errors produced by the new scheme are much smaller than those produced by the standard z-partial step scheme at a comparable vertical resolution. In particular, the new scheme shows superiority in simulating the formation of a cold intermediate layer in the ocean interior and in representing dense water cascading down a steep topography. Chapter 4 deals with the numerical modelling of the Black Sea hydrodynamics. The Black Sea is one of the largest land-locked basin in the world. Due to the vulnerability of its unique marine ecosystem, accurate long-term modelling of its hydrodynamics is needed. Any ocean model contains inaccuracies which deviate simulations from reality and data assimilation (DA) is a widely used method to improve model results. Whilst there is abundance of sea surface data, measurements of water column profiles to be used for DA are much scarcer. Therefore, a model which generates smaller errors in free-run (without DA) is needed. In this Chapter we first compare the skills of four NEMO based Black Sea models in free-run which use different discretization schemes. We conclude that the best results are obtained with the model (named CUR-MEs) which uses Multi-Envelope curved vertical s-levels and a curvilinear horizontal grid. It has increased horizontal resolution (≈ 950m) over the shelf-break and lower resolution (≈ 6km) in areas where the scale of relevant processes is larger (about 20 km). The Multi-Envelope system is designed to optimize the representation of the Cold Intermediate Layer (CIL). Second, we compare CUR-MEs in free-run with the CMEMS operational Black Sea model using DA (CMEMS reanalysis). We conclude that in many aspects the skills of the two models are similar, and CUR-MEs is slightly better for representing independently obtained profiles. Finally, we investigate the variability of the Mean Kinetic Energy of geostrophic currents and the CIL simulated by our CUR-MEs model and CMEMS reanalysis. In Chapter 5 we tackle the numerical modelling of the Dead Sea. From 1980s−1990s the Dead Sea water level is constantly decreasing, and currently it has an unprecedented rate of approximately 1.1 m/year. Since 2000, double-diffusive thermohaline staircases have been regularly observed during summer periods. Despite the increasing role of anthropogenic pressures, the evaporation−precipitation balance is still a significant factor which contributes to the recess of the sea level. In this Chapter we study the effect of different vertical mixing regimes on the features of Dead Sea water column and their potential impacts on its rate of evaporation. The methodology is based on simulating the evolution of the Dead Sea water column presenting thermohaline staircases with two contrasting numerical models. One is named SPP and it uses a standard vertical mixing scheme which does not take into account the presence of thermohaline staircases. The second is named MPP and it uses a vertical mixing parameterization compatible with the presence of step-like structures in the water column. Sensitivity experiments show that numerical horizontal pressure gradients errors, though small in both models, are higher in the MPP model, due to its ability to preserve the step-like structures of the initial condition which conversely are smoothed out in the SPP model. Realistic experiments indicate that, under the same atmospheric conditions, a vertical mixing regime typical of a water column presenting step-like structures might be able to reduce the heat transport to greater depths in comparison to a more diffusive diapycnal mixing, contributing to an increase of the Dead Sea water level recession by up to 0.1 m/year during the modelling period of August 2016.