Samuel Sayer and his sister Rose are British missionaries in German East Africa in August 1914. Their post and supplies are delivered by a small steamboat named the African Queen, helmed by the rough-and-ready Canadian mechanic Charlie Allnut, whose coarse behavior they stiffly tolerate.
When Charlie warns the Sayers that war has broken out between Germany and Britain, they choose to remain in Kungdu, only to witness German colonial troops burn down the village and herd the villagers away to be pressed into service. When Samuel protests, he is struck by a soldier and soon becomes delirious with fever, dying shortly afterward. Charlie helps Rose bury her brother and they escape in the African Queen.
Charlie mentions to Rose that the British are unable to attack the Germans because of the presence of a large gunboat, the Königin Luise, patrolling a large lake downriver. Rose comes up with a plan to convert the African Queen into a torpedo boat and sink the Königin Luise. After some persuasion, Charlie goes along with the plan.
Charlie encourages Rose to navigate the river by rudder while he tends the engine, and she is emboldened after they pass the first set of rapids with minimal flooding in the boat. When they pass the German fortress, the soldiers begin shooting at them, damaging the boiler. Charlie manages to reattach a pressure hose just as they are about to enter the second set of rapids. The boat rolls and pitches as it goes down the rapids, leading to more severe flooding on the deck. While celebrating their success, Charlie and Rose find themselves in an embrace and kiss. The third set of rapids damages the boat's propeller shaft. They rig up a primitive forge on shore and Charlie straightens the shaft and welds a new blade onto the propeller, allowing the two to set off again.
All appears lost when the boat becomes mired in the mud and dense reeds near the mouth of the river. With no supplies left and short of potable water, Rose and a feverish Charlie pass out, both accepting that they will soon die. Rose says a quiet prayer. As they sleep, torrential rains raise the river's level and float the African Queen into the lake.
Over the next two days, Charlie and Rose prepare for their attack. The Königin Luise returns and Charlie and Rose steam the African Queen out onto the lake in darkness, intending to set her on a collision course. A strong storm strikes, causing water to pour into the African Queen through the torpedo holes. Eventually the boat capsizes, throwing Charlie and Rose into the water. Charlie loses sight of Rose in the storm.
Charlie is captured and taken aboard the Königin Luise, where he is interrogated by German officers. Believing that Rose has drowned, he makes no attempt to defend himself against accusations of spying and the German captain sentences him to death by hanging. Rose is brought aboard the ship just after Charlie's sentence is pronounced. The captain questions her, and Rose proudly confesses the plot to sink the Königin Luise, deciding that they have nothing to lose. The captain sentences her to be executed with Charlie, both as British spies. Charlie asks the German captain to marry them before they are executed. The captain agrees, and after conducting the briefest of marriage ceremonies, is about to carry out the execution when the Königin Luise is rocked by a series of explosions, quickly capsizing. The ship has struck the overturned submerged hull of the African Queen and detonated the torpedoes. The newly married couple is able to escape the sinking ship and swim to safety together.
