In 1954, Darien Lake was excavated and filled. The lake was a popular swimming destination for many years. In 1964, investor Paul Snyder acquired a 164-acre (66.37 ha) parcel of land bordering the lake and opened a small 23-site campground and picnic area. Snyder continued acquiring more land eventually increasing his holdings to almost 1,000 acres (4.05 km2) of land which included seven lakes, the largest of which was Darien Lake. He stocked one of the smaller lakes, Trout Pond, with fish, increased the number of campsites and added activities for resort guests such as a small petting zoo, horseback and pony rides, paddleboats, skateboarding, tennis courts and miniature golf.

From the late 70s and into the early 80s, Snyder added more attractions, including a set of water slides on a hill near the park's entrance called Rainbow Mountain, creating an amusement park he named Darien Lake Fun Country. Snyder made a deal with HUSS Park Attractions, turning Darien Lake into the North American showcase for the German manufacturer's new rides. Through this deal, the park acquired rides such as the Pirate, Ranger, Thrillbilly and the Corn Popper, for use in the park and to give HUSS a location to display them to potential US and Canadian buyers. In 1982, the newly merged Arrow Huss built and opened the park's first major roller coaster, Viper.

In 1983, Snyder sold a 50% stake in the park to Funtime Inc., which also owned Geauga Lake and Wyandot Lake Park. The Fun Country was dropped from the name, and Funtime brought in some major improvements. Funtime's first purchase was the Vekoma-built Giant Wheel Ferris wheel, the showcase of the 1982 World's Fair in Knoxville, Tennessee, and the largest in the United States at the time, which was permanently installed in the park's center. At one point the largest in the country, the Giant Wheel was in operation until its closing during the 2021 season. Entertainment was also added to the park, with the construction of the Tops Jubilee Theater (now the Grande Theatre), the Lakeside Amphitheater, a large-scale concert stage on the south side of the main lake, presenting big-name acts including The Who, Alice Cooper, and Black Sabbath and Cinema 2000, a wide-angle movie theatre in the back of the park.

In the mid-to late 1980s, there was Splashmania, a water skiing show located on Fun Lake. The improvements continued throughout the 1980s and early 1990s, with the addition of a themed kids area, Adventure Land for Kids in 1988 and in 1989 Grizzly Run replaced a kids ride area that was located where a skatepark was. In 1990, six new slides were added to the back of the water slide complex and the area became known as Barracuda Bay and an extra charge was added to the waterpark as well a new locker area, food complex, shopping area and changing rooms. Following the success of a new wooden rollercoaster at Geauga Lake in 1988, Funtime contracted Dinn & Summers to build a new wooden coaster for Darien. The Predator roller coaster opened in May 1990. Around this time, Paul Snyder, sold his remaining share of the park to Funtime, turning over all control to them.

In 1992, a new style of entertainment debuted on the midway between Barracuda Bay and the Giant Wheel, a laser light show called Laser Light Fantasy (now called Ignite the Night), which included laser graphics and fireworks. The show was permanently installed in the Lakeside Amphitheater the following year, while concert events were moved to the new Darien Lake Performing Arts Center, which could hold nearly four times as many guests. In 1994, the old Rainbow Mountain waterslides were replaced with a new set called 'Cuda Falls and waterpark became included with park admission.

In 1995, growing regional park chain Premier Parks bought Funtime, Inc. and its three parks. Premier dove right into changes and additions. In 1995, Skycoaster opened located over Fun Lake. In 1996, Adventure Land was replaced by Popeye's Seaport with all new kiddie rides like a Ferris wheel made to look like barrels, a hand-cranked train ride, a submarine ride, a ship themed play place (removed in 2004), children's shows Popeye's Magic Show and Olive Oyl's Circus that featured audience volunteers, and a food stand and restrooms in the then new kiddie area in an area that was occupied by miniature golf course. A new miniature golf course opened behind the then-new kiddie area near Viper which replaced the old golf course.

A waterpark expansion with new attractions took place in 1996 and 1997 with Hook's Lagoon (opened in 1996) the Crocodile Isle wave pool (opened in 1997) took over Adventure Land's old location by Elk Lake with new changing rooms and a food stand were built, and a bridge was built to connect the Barracuda Bay slides with the then new water park area and a boat tag game was added to the midway. Three of the old Adventure Land rides were moved to another part of the park as the Tiny Trio in 1997. From 1996-1999, Premier would also install a new roller coaster each year, Nightmare at Phantom Cave in 1996, Mind Eraser in 1997, Boomerang: Coast to Coaster in 1998 and Superman Ride of Steel in 1999.

Nightmare was removed in 1998 and relocated to sister park The Great Escape. In 1998, Premier purchased Six Flags Theme Parks and began to rebrand its own parks as Six Flags. In May 1999, Six Flags Darien Lake opened under its new name, with a few major changes. Premier brought Six Flags' own character base, Looney Tunes and DC Comics, into the parks, renaming Popeye's Seaport to Looney Tunes Seaport, added a show in the vacant former Nightmare at Phantom Cave building called the Batman Thrill Spectacular and Hydro Force, Pipeline Plunge, Riptide Run and Torpedo Rapids were removed from Barracuda Bay and Scrambler replaced Cinema 2000. The midway stage was added to replace the boat tag game and The Emporium gift shop opened in Lasso's old location, Crazy Quilt was removed and replaced with Lasso. Premier Parks formed in 2000, assuming the name "Six Flags Inc." and adding new attractions. The next major attractions installed the Twister in 2000 and Shipwreck Falls in 2002, replacing the old Cascade Canyon water slides on the east side of Barracuda Bay as well as Slingshot behind the 'Cuda Falls water slides; and the Tornado in 2005.

2006 was a year of turmoil for Six Flags and its parks. For the 2006 season, Six Flags moved the Big Kahuna, a family-sized waterslide, from Six Flags AstroWorld to Darien Lake and also moved the Batman The Escape roller coaster from Astroworld into storage at Darien Lake, with possible plans to build it. They also added an opportunity to meet with the entire Justice League at the park. Only a month into the season, however, Six Flags began pulling back the Justice League from Darien Lake and announced Darien Lake, along with eight other parks, was being considered for sale. Many parks throughout the chain, not just those for sale, also experienced numerous changes and cutbacks throughout the summer.

In October 2006, after shortened operating hours and seasons, Six Flags officially announced the parks were being offered for sale as a package. Paul Snyder stated in a radio interview he would have considered purchasing Darien Lake from Six Flags if they allowed the parks to be sold individually. In January 2007, Six Flags announced a potential sale of seven of the parks to a new company, PARC 7F (officially called PARC Management). Six Flags chose to retain two parks it had originally considered for sale.

In April 2007, Six Flags completed the sale of Darien Lake and six other parks to PARC Management. Upon completion of the sale, PARC entered into a fifty-year contract with CNL Income Properties, under which CNL purchased the properties from and lease them back to PARC for operation.

Because of the timing of the final sale with respect to the park's opening, PARC was unable to make any major changes for the 2007 season. The biggest changes for the season were the addition of an all-new show, Le Grande Cirque, which replaced the Batman Thrill Spectacular, and the removal of all Six Flags-, Looney Tunes- and DC Comics-themed signage and references. In 2008, the park debuted the Orange County Choppers MotoCoaster, its first launched rollercoaster. A Zamperla Motocoaster coaster, it was the prototype that had been running outside Zamperla's factory in Italy. PARC pledged to lower admission prices that had risen under Six Flags ownership. Floodgate Falls was closed.

In March 2010, Darien Lake expanded its current waterpark to Six Flags Hurricane Harbor (Darien Lake) (featuring several new attractions and a repaint of the 'Cuda Falls waterslide complex in Barracuda Bay), a new 16-foot-wide (4.9 m) lazy river called Flotation Station, Swirl City slide complex (with four new slides) and a kiddie wave pool called Lazy Days Lagoon.: 127  2010 also brought about some minor park changes such as Viper being repainted with a black track, The Predator getting new trains and the addition of the Critter Chase in Adventure Isle replacing Raft Adventure.

CNL subsequently announced that it had reached an agreement to terminate PARC's lease of Darien Lake and up to 17 other locations. The move was made after, according to their 2010 SEC filings, PARC defaulted on their lease obligations.

In 2011, Herschend Family Entertainment assumed day-to-day operation and management of Darien Lake and Elitch Gardens. Rowdy's Ridge opened in 2012 with several family rides.

For the 2013 season, Blast Off was placed in the newly rethemed Waterfront Boardwalk area, which included major renovations to rides like the Grand Carousel and the Giant Wheel, along with some new dining options. Laserblast received new improvements and was rebranded Ignite the Night. UFO and the 'Cuda Falls waterslides were closed and removed. The Scrambler ride returned after two years in storage.

Herschend Family Entertainment's lease ended after the 2014 season and was taken over by Premier Parks, LLC. New rides installed during this period include Rolling Thunder, a 72-foot Larson 22M Giant Loop; Brain Drain, a set of two body slides that drops riders through a trapdoor at high speeds; and Ripcurl Racer, a six-lane Proslide Kracken Racer. Following the 2016 season, CNL Lifestyle sold Darien Lake and 14 other amusement parks to EPR Properties. The park continued to be leased and operated by Premier Parks, with no immediate change in operations or staffing. Tantrum, a Gerstlauer Euro-Fighter coaster, opened for the 2018 season.

In May 2018, Six Flags Entertainment Corporation acquired lease rights to operate the park, with the park remaining under the ownership of EPR Properties. Six Flags SkyScreamer, a Funtime Star Flyer, opened for the 2019 season. During this season, the park reverted to the Six Flags Darien Lake branding. For the 2020 season, it was announced that Wahoo Wave, a ProSlide waterslide, would be added to the newly re-named and re-themed Hurricane Harbor WaterPark.

However, the park was temporarily closed due to the COVID-19 pandemic (except for the campgrounds and Darien Square), with no timeframe from the state of New York on when theme parks can open. Despite this, the park announced on September 11, 2020, the park would remain closed and all season passes and tickets would be carried over to the 2021 season.