The Mallards, a family of ducks in Boston, block traffic and quack. The neighborhood police officer, Officer Michael, interferes and takes the audience to the beginning of the story. He introduces the audience to the Boston Public Garden: a place for Bostonians to escape the chaos of city life ("When You’ve Got A Park").

Soon-to-be parents to ducklings, Mr. and Mrs. Mallard, crash land in the park. They bicker over if they should stay to raise their ducklings. Officer Michael hears them fighting and commands them to stop by threatening a ticket ("Loud Loud Loud"). Mr. and Mrs. Mallard go for a swim to find food and are given peanuts by a kid. They agree that a tree-covered, cozy island like the one in the park could be the perfect place to raise their ducklings ("When You’ve Got A Park (Reprise)"). However, after further exploration, they realize the park might be too busy for their ducklings.

The ducks encounter Mick ("Introducing Mick"), the street sweeper who tells them to check the State House on Beacon Hill for a suitable place to begin their nest. Mr. and Mrs. Mallard fly to the State House. They notice it is full of anxious, angry politicians and will be too loud for their ducklings ("Just a Little Bit"), so they fly back to Mick for more advice. Mick tells them the Charles River might be a better option for a quiet place to nest. Mick takes them there; it’s not too busy nor too noisy - perfect for their ducklings. They fantasize about making this island home for their perfect ducklings ("No Complaints"). As they get lost in their fantasies, they argue about their ducklings' future. Will they be attending Quackvard or QIT? After Mick returns home for supper, the Mallards set up their nest on the island in Charles River for their ducklings, and Mrs. Mallard lays eight eggs ("Make Way for Ducklings"). Mrs. Mallard lays on the eggs patiently waiting for them to hatch. Jack, Pack, Lack, Kack, Mack, Nack, Ouack, & Quack are born!

Mr. and Mrs. Mallard teach their new ducklings how to be ducks: swimming and waddling. They bicker relentlessly over what to teach the children first ("Follow My Example"). As they learn, the ducklings follow in their parents’ footsteps, sparking arguments and mischief. Mr. Mallard brings the ducklings delicious, nutritious green worms to snack on. While the ducklings snack, Mr. Mallard tells Mrs. Mallard this island has become too small for their family. Mrs. Mallard refuses to leave as they hatched their ducklings there. Captain Mike crashes into their island ("The Water is Wide") and takes the ducks on an adventure upstream to explore possibilities for bigger islands to inhabit. The adventure upstream is through the winding river full of boats, both exciting but also dangerous - sparking yet another argument between Mr. and Mrs. Mallard. They eventually settle and decide to return to the first island in the Public Garden.

The Mallards set off for the Public Garden and find themselves in the middle of a crosswalk. To avoid a massive collision, cars hit their brakes and drivers shout at the ducks while the ducks quack back. Officer Michael whistles to put a halt to the commotion, telling them arguing is clearly going to get them all hurt. Mr. and Mrs. Mallard realize their arguing has not only put their ducklings in danger, but the ducklings are doing what they’ve been trying to teach them all along: following their example by arguing with each other ("Finale"). Mr. and Mrs. Mallard apologize and conced that there’s a polite way to disagree, which they haven’t been doing. The family continues waddling onto the Boston Public Garden where they make their new home.