Short answers, pulled from the story.
An estuary is a semi-enclosed coastal body of water with a free connection to the open sea, where seawater is measurably diluted with freshwater from land drainage. The word derives from the Latin aestuarium, meaning tidal inlet of the sea. A broader definition also includes fjords, lagoons, river mouths, and tidal creeks where freshwater inflow may not be perennial.
Most estuaries formed during the Holocene epoch, roughly 10,000 to 12,000 years ago, when rising sea levels flooded river-eroded or glacially scoured valleys as the last ice sheets retreated.
The four main types are drowned river valleys (coastal plain estuaries), bar-built or lagoon-type estuaries, fjord-type estuaries, and tectonically produced estuaries. San Francisco Bay is a tectonically produced example, formed by movements of the San Andreas Fault system. Fjord-type estuaries can reach depths exceeding 300 metres and are found along the coasts of Alaska, Norway, Chile, and New Zealand, among others.
Estuaries are highly productive because the mixing of freshwater and saltwater delivers high levels of nutrients both in the water column and in sediment. The commercial fishing industry draws approximately 68 percent of its total catch by value from estuaries.
Eutrophication, driven primarily by excess nitrogen in temperate estuaries, triggers algal overgrowth followed by decomposition that strips dissolved oxygen from the water, creating hypoxic zones. It weakens the root systems of salt marsh cordgrass and mangroves by shifting growth toward above-ground biomass, and can cause local animal extinctions, as seen with whitefish species in the European Alps.
Overfishing, pollution from sewage and agricultural runoff, deforestation, soil erosion, and the construction of dams and dikes all degrade estuaries. Contaminants including plastics, heavy metals, pesticides, and dioxins accumulate in estuarine sediment and in the tissues of aquatic life through bioaccumulation. Dams and diversions have reduced the Colorado River Delta in Mexico from marshlands and forests to essentially a salt flat.