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Alameda occupies what was originally a peninsula connected to Oakland. Much of it was low-lying and marshy. The higher ground nearby and adjacent parts of what is now downtown Oakland were the site of one of the largest coastal oak forests in the world. Spanish colonists called the area Encinal, meaning "forest of evergreen oak".Alameda is Spanish for "grove of poplar trees" or "tree-lined avenue." It was chosen as the name of the city in 1853 by popular vote.

The inhabitants at the time of the arrival of the Spanish in the late 18th century were a local band of the Ohlone tribe. The peninsula was included in the vast Rancho San Antonio granted in 1820 to Luis Peralta by the Spanish king who claimed California. The grant was later confirmed by the Republic of Mexico upon its independence in 1821 from Spain.

Over time, the place became known as Bolsa de Encinal or Encinal de San Antonio.

The city was founded on June 6, 1853, after the United States acquired California following the Mexican-American War of 1848. The town originally contained three small settlements. "Alameda" referred to the village at Encinal and High streets, Hibbardsville was located at the North Shore ferry and shipping terminal, and Woodstock was on the west near the ferry piers of the South Pacific Coast Railroad and the Central Pacific. Eventually, the Central Pacific's ferry pier became the Alameda Mole, featuring transit connections among the San Francisco ferries, local trollies, and Southern Pacific (formerly Central Pacific) commuter lines.

The first post office opened in 1854. The first school, Schermerhorn School, was opened in 1855 (and eventually was renamed as Lincoln School); Encinal School was opened in 1860 (and closed in 1980). The San Francisco and Alameda Railroad opened the Encinal station in 1864. The Encinal area was also known as Fasskings Station in honor of Frederick Louis Fassking. Encinal's own post office opened in 1876, was renamed West End in 1877, and closed in 1891. The West End area was originally called Bowman's Point in honor of Charles G. Bowman, an early United States settler.

On September 6, 1869, the Alameda Terminal made history; it was the site of the arrival of the first train via the First Transcontinental Railroad to reach the shores of San Francisco Bay, thus achieving the first coast to coast transcontinental railroad in North America. The transcontinental terminus was switched to the Oakland Pier two months later, on November 8, 1869.

The borders of Alameda were made coextensive with the island in 1872, incorporating Woodstock into Alameda. In his autobiography, writer Mark Twain described Alameda as "The Garden of California."

In 1917, a private entertainment park called Neptune Beach was built in the area now known as Crab Cove. Often compared to Coney Island in Brooklyn, New York, the park was a major recreation destination in the 1920s and 1930s. The original owners, the Strehlow family, partnered with a local confectioner to create treats unique to Neptune Beach. Both the American snow cone and the popsicle were first sold at Neptune Beach. The Kewpie doll, hand-painted and dressed in unique hand-sewn dresses, became the original prize for winning games of chance at the beach – another Neptune Beach innovation. The Strehlows owned and operated the beach on their own. They filled in a section of the bay to add an additional Olympic-size swimming pool and a roller coaster, which must have given riders a tremendous view of the bay. The Cottage Baths were available for rent.

Neptune Beach's two large outdoor pools hosted swimming races and exhibitions by such notable swimmers such as Olympian Johnny Weissmuller and Jack LaLanne. Weissmuller later starred in films as the original Tarzan character. LaLanne started a longlasting chain of health clubs and appeared on television. The park closed down in 1939 because the Great Depression left many people without much money, the completion of the San Francisco–Oakland Bay Bridge changed traffic patterns, people avoided paying the admission price, and the rise of car culture gave people many more choices for recreation destinations.

Once the Bay Bridge was complete, the rail lines, which ran past the entrance to Neptune Beach on the way to the Alameda Mole and the Ferry, lost passengers in great number as people shifted to automobiles. People began using their cars to escape the city and the close suburbs like Alameda and traveled further afield in California. More distant locations appealed to cash-rich San Francisco tourists in the postwar years. Youngsters in town became aware of ways to avoid paying the dime for admission to the park. Strong swimmers or waders could sneak in on the bayside just by swimming around the fence.

Some resort homes and buildings from the Neptune Beach era still exist in present-day Alameda. The Croll Building, on the corner of Webster Street and Central Avenue, was the site of Croll's Gardens and Hotel, used as training quarters for some of the greatest fighters in boxing history from 1883 to 1914. James J. Corbett, Bob Fitzsimmons, Jim Jeffries, Jack Johnson, and several other champions all stayed and trained here. Today, this preserved building has been adapted for retail and restaurants. Neptune Court, a block away on the corner of Central and McKay avenues, is also a surviving building from the resort era.

The vast majority of the Neptune Beach structures – the hand-carved carousel from the world-famed Dentzel Company, the Ferris wheel, the roller coaster, and other rides – were auctioned off in 1940, yielding pennies on the dollar of their original cost. the city did not construct any swimming facilities or develop a local beach to replace that of Neptune Beach.

When the railroad came to town in 1860s, Park Street developed as the major thoroughfare of the city. After the main Alameda train station was located here, residents of Old Alameda pulled up stakes and moved across town to the new downtown. The street's location was chosen by two landowners who wished to attract tenants and development to their land. They designated their mutual property line as Park Street.

The need for expanded shipping facilities and increased flow of current through the estuary led to the dredging of a tidal canal through the marshland between Oakland and Alameda. Construction started in 1874, but it was not completed until 1902, resulting in Alameda becoming an island.

Most of the soil from the canal dredging was used to fill in the nearby marshland. The area of Alameda called Bay Farm Island is no longer an island but is attached by fill to Oakland. In his youth, author Jack London was known to take part in oyster pirating in the highly productive oyster beds near Bay Farm Island, today long gone.

The Alameda Works Shipyard was one of the largest and best-equipped shipyards in the country. Together with other industrial facilities, it became part of the defense industry buildup before and during World War II, which attracted many African-American and European-American migrants from other parts of the United States for the high-paying jobs. In the 1950s, Alameda's industrial and shipbuilding industries thrived along the Alameda Estuary. This was the site of operation of the world's first-ever, land-based, containerized shipping crane.

In the early 21st century, the Port of Oakland, across the estuary, has become one of the largest ports on the West Coast. Its operators use shipping technologies originally experimented within Alameda. As of March 21, 2006, Alameda is a "Coast Guard City", one of seven then designated in the country. As of 2018, it is one of twenty-one within the country.

In addition to the regular trains running to the Alameda Mole, Alameda was also served by local steam commuter lines of the Southern Pacific (initially, the Central Pacific). Alameda was the site of the Southern Pacific's West Alameda Shops, where all the electric trains were maintained and repaired. These were later adapted as the East Bay Electric Lines. Southern Pacific's electrified trains were not streetcars, but full-sized railroad cars that connected to the mainland via bridges at Webster Street and Fruitvale (only the latter bridge survives today). The trains ran to both the Oakland Mole and the Alameda Mole. A line that ran between the two moles was dubbed the "Horseshoe Line" for the shape of the route on a map. Soon after completion of the Bay Bridge, Alameda trains connected directly to San Francisco by the lower deck of the bridge. The ferries became unnecessary.

In the 1930s Pan American Airways established a seaplane port along with the fill that led to the Alameda Mole. This was the original home base for the China Clipper flying boat. In 1929, the University of California established the San Francisco Airdrome located near the current Webster Street tube as a public airport. The Bay Airdrome had its gala christening party in 1930. The airfield was a busy place, as an early home base for Coastal Air Freight, Varney Air Lines, West Coast Air Transport, Western Air Express, the Transbay Air Ferries, and Boeing's Pacific Air Transport. The Airdrome was closed in 1941 when its air traffic interfered with the newly built Naval Air Station Alameda (NAS Alameda). With the advent of World War II, a vast stretch of the marshy area southwest of the Alameda Mole was filled and the NAS Alameda established. This major Naval facility included a large airfield, as well as docks for several aircraft carriers. It closed in 1997.

Starting in the 1940s and continuing into the 1970s, multiple proposals were considered to build a highway bridge from Alameda to the San Francisco Peninsula, known as the Southern Crossing.

The Bay Area Rapid Transit is currently studying the creation of a second Transbay Tube; some potential alignments would bring BART service to Alameda Island.

In the late 1950s, the Utah Construction Company began a landfill beyond the Old Sea Wall and created South Shore.

On February 7, 1973, a USN Vought A-7E Corsair II fighter jet on a routine training mission from Lemoore Naval Air Station suddenly caught fire, 28,000 ft (8,534 m) over the San Francisco Bay and crashed into the Tahoe Apartments in Alameda. Eleven people, including pilot Lieutenant Robert Lee Ward, died in the crash and fire.

The 2010 United States Census reported that Alameda had a population of 73,812. (2015 census estimates place the population at 78,630)

The population density was 3,214.9 people per square mile (1,241.3/km²). The racial makeup of Alameda was 37,460 (50.8%) White, 23,058 (31.2%) Asian, 4,759 (6.4%) African American, 426 (0.6%) Native American, 381 (0.5%) Pacific Islander, 2,463 (3.3%) from other races, and 5,265 (7.1%) from two or more races. Hispanic or Latino of any race were 8,092 persons (11.0%).

The Census reported that 72,316 people (98.0% of the population) lived in households, 857 (1.2%) lived in non-institutionalized group quarters, and 639 (0.9%) were institutionalized.

There were 30,123 households, out of which 9,144 (30.4%) had children under the age of 18 living in them, 13,440 (44.6%) were opposite-sex married couples living together, 3,623 (12.0%) had a female householder with no husband present, 1,228 (4.1%) had a male householder with no wife present. There were 1,681 (5.6%) unmarried opposite-sex partnerships, and 459 (1.5%) same-sex married couples or same-sex partnerships. 9,347 households (31.0%) were made up of individuals, and 2,874 (9.5%) had someone living alone who was 65 years of age or older. The average household size was 2.40. There were 18,291 families (60.7% of all households); the average family size was 3.06.

The age distribution of the population shows 15,304 people (20.7%) under the age of 18, 5,489 people (7.4%) aged 18 to 24, 21,000 people (28.5%) aged 25 to 44, 22,044 people (29.9%) aged 45 to 64, and 9,975 people (13.5%) who were 65 years of age or older. The median age was 40.7 years. For every 100 females, there were 91.7 males. For every 100 females age 18 and over, there were 88.5 males.

Per capita money income in past 12 months (2013 dollars), 2009 – 2013 was $41,340.00 per US Census. Median household income, 2009 – 2013 was $74,606.00 per US Census.

There were 32,351 housing units at an average density of 1,409.0 per square mile (544.0/km²), of which 30,123 were occupied, of which 14,488 (48.1%) were owner-occupied, and 15,635 (51.9%) were occupied by renters. The homeowner vacancy rate was 1.1%; the rental vacancy rate was 5.7%. 37,042 people (50.2% of the population) lived in owner-occupied housing units and 35,274 people (47.8%) lived in rental housing units.

As of the census of 2000, there were 72,259 people, 30,226 households, and 17,863 families residing in the city. The population density was 2,583.3/km² (6,693.4/mi²). There were 31,644 housing units at an average density of 1,131.3/km² (2,931.2/mi²). The racial makeup of the city was 56.95% White, 6.21% Black or African American, 0.67% Native American, 26.15% Asian, 0.60% Pacific Islander, 3.29% from other races, and 6.13% from two or more races. 9.31% of the population were Hispanic or Latino of any race.

There were 30,226 households, out of which 27.7% had children under the age of 18 living with them, 43.7% were married couples living together, 11.4% had a female householder with no husband present, and 40.9% were non-families. 32.2% of all households were made up of individuals, and 9.4% had someone living alone who was 65 years of age or older. The average household size was 2.35 and the average family size was 3.04.

In the city, the age distribution of the population shows 21.5% under the age of 18, 7.0% from 18 to 24, 33.6% from 25 to 44, 24.6% from 45 to 64, and 13.3% who were 65 years of age or older. The median age was 38 years. For every 100 females, there were 92.3 males. For every 100 females age 18 and over, there were 89.5 males.

The median income for a household in the city was $56,285, and the median income for a family was $68,625. Males had a median income of $49,174 versus $40,165 for females. The per capita income for the city was $30,982. About 6.0% of families and 8.2% of the population were below the poverty line, including 11.4% of those under age 18 and 6.1% of those age 65 or over.

There is a large Filipino community; and also a major Portuguese community, from which Tom Hanks' mother came and where Lyndsy Fonseca was raised for some time. Alameda also has a historic Japanese American community and had a small Japanese business district on a portion of Park Street before World War II, when the city's Japanese population was interned. A Japanese Buddhist church is one of the few remaining buildings left of Alameda's pre-war Japanese American community.

In 1997 he became one of San Francisco's youngest members of the board of Supervisors,serving a full term from 1998 to 2002. San Francisco's 49th Lieutenant Governor, and California's 40th Governor.