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This work is focused on the application of a modelling system to simulate 3-D interaction between the Curonian Lagoon and the Baltic Sea coastal waters and to reflect spatiotemporal dynamics of marine waters in the Curonian Lagoon. The model system is based on the finite element programme package SHYFEM which can be used to resolve the hydrodynamic equations in lagoons, coastal seas, estuaries and lakes. The results of a one year (2009) 3-D model simulation with real weather and hydrological forcing show that the saline water intrusions from the sea through Klaipėda Strait are gradually decreasing with distance from the sea and become negligible (average annual salinity about 0.57‰) at a distance of about 20 km to the south of Kiaulės Nugara island. Analyses of the simulation results also show this area to be highly heterogeneous according to the vertical salinity distribution. While in the deeper Klaipėda Strait (harbour waterway) differences in average salinity between near bottom and surface layers varies in the range 2–2.5‰, in the rest of the Curonian Lagoon it is less than 0.5‰. The exchange flow showed vertical structure, but was horizontally uniform with the presence of a two-directional flow that from time to time changes to either saline water one-directional flow to the Curonian Lagoon or fresh water one-directional flow to the sea. Two-directional flow duration decreases with a distance from sea entrance in Klaipėda Strait from around 180 days yr−1 close to the sea entrance to 50 days yr−1 just behind Kiaulės Nugara island. One-directional outflow duration is increasing with a distance from the sea entrance from 100 to 225 days yr−1. One-directional inflow duration occurs in the range of 70–100 days yr−1. The analysis of the ratio of buoyancy layer thickness to water depth (hb/H) and the Wedderburn number identified the main importance of wind action on the flow structure. Strong winds from the North and NW determine a barotropic inflow which is mostly responsible for the salt water intrusion into the Curonian Lagoon. Absence of wind or cross-strait wind regimes allows the maintenance of a two-layer flow typical of estuarine dynamics.

Boka Kotorska Bay, located in the southeastern Adriatic Sea along the Montenegro coastline, is a complex morphological structure, consisting of three embayments. They are connected and interact with the sea through narrow straits and the bay can be considered one of the main freshwater inputs into the southern Adriatic Sea. In the framework of the ADRICOSM-STAR project, a hydrodynamical model of this region provided results that are compared with CTD data and hydrodynamic scenarios are discussed for the bay. A finite element coastal model nested in a finite difference model that runs on the Adriatic Sea has been used to reproduce the complex morphology of the bay. Hydrodynamic modeling allows studying the main characteristics of this bay, identifying it as a Region of Freshwater Influence (ROFI). The freshwater input coming from the numerous sources present in the bays can strongly modify temperature, salinity and current patterns. The computation of the buoyancy ratio of the thermal and haline buoyancy flux showed that the Kotor and Morinj Bays experience a major effect of surface heating in summer, while the rest of the bay seems to be mostly affected by freshwater influence from precipitation and river discharge. An average estuarine situation is seen, presenting a surface outflow and a bottom inflow of water. Specific hydrodynamic processes can be detected in the channels that connect the different sub-basins of the Boka Kotorska Bay. Moreover, the computation of the Kelvin number in correspondence of the internal straits suggests classifying the Kotor and Morinj Bays differently from the outermost areas. The innermost Kotor and Morinj Bays, generally exchange little water with the sea and they have high values of residence times. However, their fresh water springs and rivers have the highest discharges that can change abruptly the picture with increase of the total water exchange between the bay and the sea.