Brackish lagoon with breeding islets, saltmarshes and mudflats, overgrown by different types of halophytes, covers nearly three-quarters of the reserve area. It is characterized by many lagoon elements, such as the central area of deep water, the network of secondary ditches, shallows and tidal plains without vegetation as well as islets and mudflats with halophytic vegetation that direct water currents caused by wind and tides.
The lagoon floor gradually rises from the central area of deep water towards the coast through the system of secondary ditches and shallows, extending to the area of tidal plains and mudflats with shoreline vegetation. Brackish part of the reserve is supplied both with sea and fresh water. The sea channel which passes through the Port of Koper connects the lagoon with the sea, while on the east side the Rižana River flows in through its left discharging channel. The lagoon represents a diverse mix of at least five habitat types protected at European level in the Natura 2000 network. The entire lagoon water body is a priority habitat type coastal lagoon (Natura 2000 Code 1150*), as rare European shallow sea water areas, at least partially separated from the sea, are defined.