In addition to classifying estuaries based on their geology, scientists also classify estuaries based on their water circulation. The five major types of estuaries classified according to their water circulation include salt-wedge, fjord, slightly stratified, vertically mixed, and freshwater.

Water movements in estuaries transport organisms, circulate nutrients and oxygen, and transport sediments and wastes. Once or twice a day, high tides create saltwater currents that move seawater up into the estuary. Low tides, also once or twice a day, reverse these currents. In some estuaries, the mixing of fresh water from rivers and saltwater from the sea is extensive; in others it is not. In the Hudson River in New York, for example, tidal currents carry saltwater over 200 km upstream.

Coastal plain estuaries, or drowned river valleys, are formed when rising sea levels flood existing river valleys. Bar-built estuaries are characterized by barrier beaches or islands that form parallel to the coastline and separate the estuary from the ocean. Barrier beaches and islands are formed by the accumulation of sand or sediments deposited by ocean waves.

The daily mixing of fresh water and saltwater in estuaries leads to variable and dynamic chemical conditions, especially salinity. When fresh water and saltwater meet in an estuary, they do not always mix very readily. Because fresh water flowing into the estuary is less salty and less dense than water from the ocean, it often floats on top of the heavier seawater. The amount of mixing between fresh water and seawater depends on the direction and speed of the wind, the tidal range (the difference between the average low tide and the average high tide), the estuary’s shape, and the volume and flow rate of river water entering the estuary. These factors are different in each estuary, and often change seasonally within the same estuary. For example, a heavy spring rain, or a sustained shift in local winds, can drastically affect the salinity in different parts of an estuary.

The degree to which fresh water and saltwater mix in an estuary is measured using isohalines. Isohalines are areas in the water that have equal salt concentrations, or salinities. The shape of the isohalines indicates the amount of mixing that is occurring, and may provide clues about the estuary’s geology. To determine isohalines, scientists measure the water's salinity at various depths in different parts of the estuary. They record these salinity measurements as individual data points. Contour lines are drawn to connect data points that have the same salinity measurements. These contour lines show the boundaries of areas of equal salinity, or isohalines, and are then plotted onto a map of the estuary. The shape of the isohalines tells scientists about the type of water circulation in that estuary.

Salt-wedge Estuaries

Salt-wedge estuaries are the most stratified, or least mixed, of all estuaries (Molles, 2002; Ross, 1995). They are also called highly stratified estuaries. Salt-wedge estuaries occur when a rapidly flowing river discharges into the ocean where tidal currents are weak. The force of the river pushing fresh water out to sea rather than tidal currents transporting seawater upstream determines the water circulation in these estuaries. As fresh water is less dense than saltwater, it floats above the seawater. A sharp boundary is created between the water masses, with fresh water floating on top and a wedge of saltwater on the bottom. Some mixing does occur at the boundary between the two water masses, but it is generally slight. The location of the wedge varies with the weather and tidal conditions. Examples of salt-wedge estuaries are the Columbia River in Washington and Oregon, the Hudson River in New York, and the Mississippi River in Louisiana.

Fjord-type Estuaries

Fjords (pronounced fee-YORDS) are typically long, narrow valleys with steep sides that were created by advancing glaciers. As the glaciers receded they left deep channels carved into the Earth with a shallow barrier, or narrow sill, near the ocean. The sill restricts water circulation with the open ocean and dense seawater seldom flows up over the sill into the estuary. Typically, only the less dense fresh water near the surface flows over the sill and out toward the ocean. These factors cause fjords to experience very little tidal mixing; thus, the water remains highly stratified. Fjords are found along glaciated coastlines such as those of British Columbia, Alaska, Chile, New Zealand, and Norway.

Slightly Stratified Estuaries

In slightly stratified or partially mixed estuaries, saltwater and freshwater mix at all depths; however, the lower layers of water typically remain saltier than the upper layers. Salinity is greatest at the mouth of the estuary and decreases as one moves upstream. Very deep estuaries, such as Puget Sound in Washington State and San Francisco Bay in California, are examples of slightly stratified estuaries. Even though Puget Sound is classified as a fjord in terms of its geology, it does not exhibit the characteristics of a fjord when classified by water circulation.

Vertically Mixed Estuary

A vertically-mixed or well-mixed estuary occurs when river flow is low and tidally generated currents are moderate-to-strong. The salinity of water in a vertically-mixed estuaries is the same from waters surface to the bottom of the estuary. Strong tidal currents eliminate the vertical layering of freshwater floating above denser seawater, and salinity is determined by the daily tidal stage. An estuary's salinity is highest nearest the ocean and decreases as it moves up the river. This type of water circulation might be found in large, shallow estuaries, such as Delaware Bay.

Freshwater Estuaries

We normally think of estuaries as places where rivers meet the sea, but this is not always the case. Freshwater or Great Lakes-type estuaries do not fit the definition of a brackish water estuary where freshwater and seawater mix.

Freshwater estuaries are semi-enclosed areas of the Great Lakes in which the waters become mixed with waters from rivers or streams. Although these freshwater estuaries do not contain saltwater, they are unique combinations of river and lake water, which are chemically distinct. Unlike brackish estuaries that are tidally driven, freshwater estuaries are storm-driven. In freshwater estuaries the composition of the water is often regulated by storm surges and subsequent seiches (vertical oscillations, or sloshing, of lake water). While the Great Lakes do exhibit tides, they are extremely small. Most changes in the water level are due to seiches, which act like tides, exchanging water between the river and the lake.

Old Woman Creek is a freshwater estuary located on the south-central shore of Lake Erie in Ohio. Tidal changes in water level only average about 3 cm. As a storm-driven estuary system, during periods of low water flow, a barrier sand beach will often close the mouth of the estuary, isolating it from Lake Erie.