The theme of conflict is rife throughout the novel The River Between. Many characters and groups are in intrinsic conflict with one another or have personal conflict with other individuals, and it all serves to highlight the cultural differences that appear in the novel.

First, there is a religious difference between the Christian groups (such as those in charge of the Siriana Mission School) and the indigenous peoples. There are stark cultural differences that cause conflict—most glaringly when Joshua’s daughter, Muthoni, decides to undergo female genital mutilation, or female circumcision, which is against the Christian teachings of the school but is a coming-of-age practice in the tribe. She is expelled from the school for this practice.

The interpersonal conflicts show up just as strongly. Chege and Joshua have an ongoing rivalry, and the two lead opposing clans in the tribe, with Chege attempting to hold on to the traditions of the past and Joshua striving to become like the Europeans. Additionally, there is great personal conflict as many of the characters attempt to deal with their personal feelings and understanding of the culture war—such as Nyambura, who is trying to remain consistent with tribal practices but is failing. She is unable to attend all of the tribal meetings and feels great remorse and pain at letting her clan down.

Interestingly, the primary conflict in the novel The River Between revolves around the rivalry between the locals themselves (i.e., the people living in Kameno do not share the same ideologies as those living in Makuyu), as opposed to that between the locals and the Christian missionaries. Ngugi, the author of the novel, notes that the rivalry between the two sides is deeply rooted in the past of the Kikuyu people, and it attracts significant attention when the ideologies of the white people, primarily through Christian teachings, are imposed on the Kikuyu people. Chege leads the conservatives in their endeavors and further emphasizes on the importance of keeping their traditional teachings and values alive. More often than not, he cautions his people to be on the lookout for the advent of the white people. He says:

Now, listen my son. Listen carefully, for this is the ancient prophecy...I could not do more. When the white man came and fixed himself in Siriana, I warned all the people. But they laughed at me. Maybe I was hasty. Perhaps I was not the one...

On the other hand, Joshua leads his clansmen in adopting the Europeans’ way of life. He is overzealous in spreading Christianity among his people.

Other forms of conflict evident in the novel ensue as a result of the rivalry or struggle between an individual and the Kikuyu community. For instance, Waiyaki fails to consult with the community’s elders before building more schools. Though his intentions were not ill, the elders feel undermined and resolve to punish him. Likewise, Muthoni resists Christian teachings and decides to get circumcised so that she can be accepted by the tribe.