When a river runs down out of a mountain, and hits a low, flat area just before reaching the ocean, it causes the water to back up and fan out into many small "sloughs".
In the case of the California Delta, there are many rivers that come out of the Sierra Mountains. The largest rivers are the Sacramento River (flowing out of the dam at Shasta Lake), the San Joaquin (flows through Stockton) and the Mokelumne River. They, along with a dozen smaller rivers, all converge in the "central valley" before flowing out to the San Francisco Bay.
All of this water is essentially at sea level. Stockton is considered a deep water port, and large ships routinely follow the channel from the ocean, through the bay and on up to Stockton.
Back in 1850, using cheap Chinese labor, they built a series of levees that restricted the water to the major sloughs and claimed the land for farming. Back before 18 wheel trucks and freeways this was very valuable land: water for irrigation (it doesn't rain enough in California to grow crops without irrigation) and easy transportation (crops were loaded onto barges and floated down to San Francisco).
In the last 50 years the advancement of paved roads and efficient trucks have eliminated the barges as transportation. As a result, some of the tracts of land have lost their "premium" value, especially the tracts that don't have bridges linking them (ferries are still required to reach some of the islands).
Occasionally a levee breaks, and a tract of land gets flooded. "Jones Tract" flooded just last June. This tract has good land access and was still valuable so it was repaired and is in the process of being pumped out. Other tracts, such as "Mildred" or "Frank's Tract" had no bridge, and was deemed not worth reclaiming when their levee's broke. These areas are now large "lake" areas within the delta.