The degree of water circulation depends on the width of the tidal inlets, the tidal range, and the amount of runoff from adjacent land areas. Maximum velocities are attained at the points where the water passes through the barriers. In the entrance to the Gippsland lagoons, for example, tidal currents reach 5.6 km (3.5 miles) per hour, but river floods that escape to the ocean can raise the velocity to 13 km (8 miles) per hour. Water may be blown into the lagoon by strong winds; the increased level results in an outflowing current when the wind drops. Seiches—that is, rhythmic oscillations of water in enclosed or partially enclosed water bodies—can be created in this way. Small waves can be generated within lagoons when the wind blows along their maximum dimension. These may reach 1.25 metres (about 4 feet) in height and 1.5 to 9 metres (about 5 to 30 feet) in length in the Gippsland lagoons. In coral atoll lagoons there is little or no runoff, and seawater moves in and out through the passes, where tidal currents reach their maxima. Velocities of 19 to 22 km (12 to 14 miles) per hour have been recorded in the Hao Channel of the Tuamotu Archipelago in French Polynesia.

A lagoon into which a major river flows is known as an estuarine lagoon and may be regarded as a special kind of estuary.

Water temperature and salinity

In the Mayotte lagoon the water has the same properties as the upper layers of the open ocean. The salinity is close to 35 parts per thousand (ppt), and the temperature varies between 27 and 24 °C (81 and 75 °F). This is typical of coral lagoons, but the temperature and salinity of barrier island lagoons are more variable because of their wider climatic range. Because they are shallow, lagoon waters approximate the air temperature: colder than the open ocean in winter, warmer in summer.

Salinities decrease as a function of the amount of runoff entering the lagoon in relation to the tidal influx. Lagoons may be considered brackish, marine, or hypersaline. Brackish lagoons receive much runoff, and salinity increases toward the tidal inlets. The Gippsland lagoons exemplify this type. The salinity at the inner end varies from 0.5 to 5 ppt according to season, and central values vary between 5 and 20 ppt.

In hot arid regions lagoons lose more water by evaporation than they receive from land drainage. This causes surface waters to become more dense than seawater and to sink to the bottom. Seawater flows in at the surface to replace that lost by evaporation, creating a circulation the reverse of that found in estuaries. If exchange with the open sea is limited, the lagoon may become much more saline than the open sea. Consequently, various species of plants and animals become adapted to life in high salinities. Laguna Madre in Texas and Syvash Sound in the Black Sea are examples of hypersaline lagoons. (They have salinities of 65 and 132 ppt, respectively.) Salt deposits may form in these conditions. The denser saline water tends to lie beneath the fresher water, where mixing is not severe.

Equilibrium bottom profiles

Lagoons behind coastal barriers normally are zones of fine sedimentation. Their bottom profiles, therefore, build up gradually with time. Typical depths of the Texas lagoons vary between 1.25 and 3.5 metres (4 and 11 feet), and their floors are flat. Early theories that attempted to relate the form of the offshore and lagoon profile are no longer held; and, because the lagoon profile changes with continued deposition, it cannot be used to establish the process of lagoon formation. The profile is usually gently undulating, but it may contain deeper channels, especially near the tidal inlets. Profiles across coral lagoons either are smooth and flat from calcareous sedimentation or contain knolls of growing or dead coral. There are 2,300 such knobs in the Enewetak Lagoon in the Marshall Islands.