A particular curiosity of Škocjanski zatok are the mudflats, overgrown with typical shoreline plants – halophytes adapted to growth in the salty ground. The lagoon floor gradually rises from the central deep water channel towards the coastal tidal area of shallows and mudflats without vegetation and further to partially flooded sand- and mudflats with annual haplophytes and semidry mudflats with perrenial halophytes which are seldom reached by the sea. Such sites are extremely rare in Slovenia and of special interest because they are found only in river floodplains of Piran, Strunjan and Koper Bay of as well as in Škocjanski zatok.
Sand- and mudflats are extremely diverse, rich and unstable habitats. They are exposed to waves and tides, and thus the large fluctuations in temperature.
Sandy and muddy bottom of tidal plains is overgrown with marine algae and seed plants, among which the ditchgrass (Ruppia maritima) is the most frequent. This place is inhabited by benthos invertebrates, several species of fish and sea plants and they represent an easily accessible food for many species of waterfowl such as herons (Ardeidae), crakes (Rallidae) and waders (Charadriiformes).