Africa, World War One; deep in the German-occupied colony, near the Uganda river, lies a remote little village where accommodations are minute grass huts built around a little wooden church. The Germans appear seemingly out of nowhere, killing the women and children, burning the huts to the ground and kidnapping the men. They disappear as quickly as they came, leaving devastation, and a village with nothing left, behind. British Missionary Reverand Samuel Sayer is so distressed by what he has witnessed that he kills himself, leaving behind his sister, Rose, to fend for herself. Rose, too, is in the depths of despair. The occupied colony is dangerous and there is a constant threat of a repeat of the German brutality. Escape is also dangerous as the only escape is via the wild and unforgiving Utanga River. If Rose can make it to Lake Victoria she might be free but standing in her way is a German gunship called the Louisa; the ship patrols the Tanganyika shore of the lake. Because of the rapids and the carnivorous species that make the Utanga River their home, the river has only been successfully traveled once, and that was more than one hundred years ago.
Rose is in shock over the death of her brother and stumbling around the billiard in a disoriented state, when a man by the name of Charlie Allnut appears out of nowhere. He is an archetypal "sea dog" of a boat captain and delivers the mail and also supplies to the village. He takes Rose on board the supply boat, named the African Queen, before the Germans come back. The boat is barely seaworthy and is a rust-bucket that runs more from a kick to the engine from Allnut than it does from good mechanics. Almost immediately Rose and Allnut disagree about where they should go; he wants to go north but she wants to go south downriver and attack the German boat. Allnut calls her a crazy old maid and she makes it plain that she thinks he is a disgrace to the naval profession because he is a coward. Surprisingly they do end up going south as ironically it is the only way to avoid the Germans and it is also the only way Allnut will get any peace from Rose's nagging.
The two make awkward traveling companions and really cannot stand each other. Rose reads her Bible all day and Allnut drinks run until he passes out. Rose is rather a Billy and whilst he is sleeping pours all of his booze into the river. This has a very negative effect on his psyche and he doesn't understand why she did it. Rose then refused to talk to him until he agrees to try to sink the Louisa. He still speaks to her but the silence is sending him slowly mad and so he agrees; he fashions torpedoes from explosives and two gas canisters that he has on board. Navigating the river with courage and skill, Allnut's seamanship starts to make Rose look at him differently. Rose starts to feel aroused by the thrill of going through the dangerous rapids but does not know the feeling and likens it instead to hearing her brother deliver a sermon whilst being consumed by the Holy Ghost. As she is telling Allnut about this they are shot at by African guerillas lurking on the riverbanks and this adrenaline rush prompts them to hug and kiss passionately; they become lovers and realize that far from hating each other they are actually madly in love.
Although their animosity has disappeared the danger has not. They run aground in the shallows and Allnut has to get into the mud to pull the African Queen back into the deeper waters. It doesn't work; they are stuck in marshes with nothing but grass surrounding them and no obvious way out. They resign themselves to death but as the lie weak and beaten on the deck it begins to rain, which raises the river and allows the African Queen to set sail again. They make it to the mouth of the Utanga River and see the Louisa on Lake Victoria for the first time. Renewed, they wait for the German ship to make its way back around on patrol. Their plan is to fasten the homemade torpedoes inside the African Queen and launch them through two holes cut above the water line; they will deliberately collide with the Louisa and the African Queen will act as a battering ram. Rose and Allnut squabble about who will stay on board until the last moment but they agree they would not want to live without the other and agree to stay on board together and jump off, hopefully to safety, at the last moment. The Louisa crew are surprised to see the boat but as they move towards their target a storm comes up, tossing the African Queen over and throwing Rose and Allnut into the lake. The Louisa is not sunk and the lovers appear to have drowned.
When there is calm again after the storm it becomes clear that Allnut is alive. The Germans have captured him and are determined to interrogate him until all their questions are answered. They threaten him with telling the truth on punishment of death but fearing his Rose drowned, Allnut doesn't care if he dies too. Then he hears Rose's voice and realizes she has also been captured. He plans on saving her by pretending they have never met but Rose can't wait to be defiant and tells the German captain they had devised a way to blow up the Louisa. The captain believes them both to be insane and decides to hang both of them. As they stand on deck waiting for their deaths, Allnut asks the captain to marry them as his last request as it would mean the world to Rose. Convinced they are completely mad the captain agrees. Before they are hung the Louisa hits the African Queen which has sunk beneath the water and it explodes. Rose and Allnut swim to safety, clinging to a plank with the name African Queen on it, all the while singing "There Was An Old Fisherman."
