The conflict in "The Man to Send Rain Clouds" is an unusual one not typically found in short story literature, which, incidentally sheds some light on--or perhaps deepens--the ambiguity of the title. Teofilo's peaceful death while tending his sheep (a Biblical and pastoral allusion) is the occasion for the conflict of the story. The Pueblo people want a traditional Pueblo religion burial service and to that end they paint Teofilo's face and wrap him in a red blanket. They attend to Teofilo's preparation and ceremony in a secretive fashion so as to not awaken the suspicions of the Catholic priest who would want to give Teofilo a Catholic burial that would not include face paint and red blankets. This is the major physical conflict: arranging Teofilo's burial according to Pueblo ways without interference from the white and Catholic world.
The metaphysical, or spiritual, conflict that goes along with this is the battle for the continued existence of Pueblo beliefs in an encroaching white society. Silko actually offers a suggested means by which the battle can be put to rest with each side standing victorious at the end. Through the character of Louise, Leon's wife, it is suggested that both cultures and both religions can co-exist and can contribute to each other. Specifically, Louise suggests that it would be good to have the priest sprinkle Teofilo's body at the time of burial with holy water so as to quench Teofilo's thirst. The Pueblo religion teaches that the living give help in relieving the dead person's need for food and drink, this is why Louise thinks of quenching the old man's thirst. The Pueblo religion also teaches that the dead bring rainclouds and rain back to the village to quench the thirst of the land. Therefore, it stands to reason that if Teofilo's own thirst is quenched with holy water, then he will be able to bring really "big thunderclouds for sure."
The resolution comes when Father Paul stands at Teofilo's grave side with the holy water and sprinkles it on Teofilo's red-wrapped body. He originally didn't want to participate in what he views as a pagan ceremony to false gods but reconsiders although he is still confused and somewhat suspicious of a prank being played upon him. When he see what the Pueblo perceive as signs of a successful offering, he is puzzled and thinks that if he could recall something he might be able to understand the near-miraculous and -supernatural results of the sprinkling of the holy water. Father Paul leaves the burial muddled and deep in thought but the villagers are content that they have found a pragmatic use for Father Paul's blessings and that the two religions and cultures have been joined as one in order to attain "big thunderclouds for sure." This pertains to the title: Who is the man who sends water? In one sense, it is Teofilo who will bring thunderclouds but, in another sense, it is the Catholic priest Father Paul who is the man who brings rainclouds because it is his holy water that is seen as adding materially to Teofilo's future success as a bringer of big rainclouds.