Samuel Sayer and his sister Rose are British Methodist missionaries in the village of Kungdu in German East Africa at the beginning of World War I in September 1914. Their mail and supplies are delivered by a small steam launch 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 forcibly recruited. When Samuel protests, he is beaten by an officer, and becomes delirious with fever and soon dies. Charlie returns shortly afterward after having found his mine to have been destroyed by the Germans and being chased for his supplies, which include gelatin explosives. He helps Rose bury her brother, and they set off in the African Queen.
While planning their escape, Charlie mentions to Rose that the British are unable to attack the Germans due to 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. Charlie points out that navigating the Ulanga River to get to the lake would be suicidal: they would have to pass a German fort and negotiate several dangerous rapids. But Rose is insistent and eventually persuades him to go along with the plan. Eventually Charlie becomes inebriated and drunkenly insults Rose and her plan, who retaliates by dumping his supply of gin into the river.
Charlie allows Rose to navigate the river by rudder while he tends the engine, and she is emboldened after they get through the first set of rapids with minimal flooding in the boat. But when they pass the fortress and the soldiers begin shooting at them, the bullets damage the boiler, although they are unable to shoot the boat severely due to the sun getting in their eyes. 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 in the boat. However, they make it through.
While celebrating their success, the two find themselves in an embrace. Embarrassed, they break off, but eventually succumb and become lovers. The third set of rapids damages the propeller shaft. Rigging up a primitive forge on shore, Charlie straightens the shaft, welds a new blade onto the prop, and they are off again.
All appears lost when the boat becomes mired in the mud and dense reeds near the mouth of the river. They try to tow the boat through the muck, only to have Charlie come out of the water covered with leeches. With no supplies left and short of potable water, Rose and a feverish Charlie pass out, both accepting they will die soon. Rose says a quiet prayer. As they sleep, exhausted and beaten, torrential rains far upstream gently raise the river’s level and float the African Queen off of the mud and into the lake. Once on the lake, they narrowly avoid being spotted by the Königin Luise.
Over the next two days, Charlie and Rose convert some oxygen cylinders into torpedoes using gelatin explosives and improvised detonators. They push the torpedoes through holes cut in the bow of the African Queen as improvised spar torpedoes. 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 which causes water to pour into the African Queen through the torpedo holes. Eventually the African Queen capsizes, throwing them both 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 the captain. 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. However, Rose is captured and brought to the Königin Luise just after Charlie’s sentence is pronounced. The captain questions her, and Rose confesses the whole plot proudly, deciding 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 executing them (even though ship captains do not in fact have that authority). After a brief marriage ceremony, there is an explosion and the Königin Luise quickly capsizes. The Königin Luise has struck the overturned submerged hull of the African Queen and detonated the torpedoes. The newly married couple happily swims to safety.