The Israelites continued their journey through the wilderness, traveling according to the LORD's command and camping at Rephidim. However, there was no water for the people to drink, and they quickly grew frustrated and began quarreling with Moses, demanding that he provide them with water. Moses, troubled by their complaints, asked them why they were quarreling with him and why they were testing the LORD.

The people's frustration escalated into open grumbling against Moses, and they questioned why he had brought them out of Egypt only to let them, their children, and their livestock die of thirst in the desert. Moses cried out to the LORD, expressing his distress and fear that the people were on the verge of stoning him.

God responded by instructing Moses to walk ahead of the people, taking along some of the elders of Israel and the staff with which he had struck the Nile River. The LORD told him to strike the rock at Horeb, promising that water would flow from it for the people to drink. Moses did exactly as the LORD commanded, in the sight of the elders of Israel. Moses named the place Massah and Meribah, meaning "testing" and "quarreling," because the Israelites had quarreled and tested the LORD, asking whether He was truly among them.

Exodus 17 then shifts to a military encounter. The Amalekites came and attacked the Israelites at Rephidim. Moses instructed Joshua to choose men and go out to fight against the Amalekites, while Moses himself would stand on top of a nearby hill with the staff of God in his hand. Joshua did as Moses commanded and engaged the Amalekites in battle. As the fighting unfolded, a remarkable pattern emerged: Whenever Moses held up his hand with the staff, Israel prevailed in the battle, but whenever he lowered his hand, the Amalekites prevailed.

As the battle wore on, Moses grew weary and his hands became heavy. Aaron and Hur, who were with him on the hill, responded by having Moses sit on a stone while they stood on either side of him and held up his hands — one on each side — keeping them steady until the sun went down. Through this sustained effort, Joshua was able to defeat the Amalekites.

Afterward, the LORD instructed Moses to write down an account of the victory as a memorial and to recite it to Joshua, declaring that He would completely blot out the memory of the Amalekites from under heaven. Moses then built an altar and called it Jehovah–nissi, which means "The Lord is my Banner," proclaiming that the LORD would be at war with the Amalekites from generation to generation.