What does 1 Samuel 3:13 mean?

The Lord is declaring a prophecy to Samuel, still a boy, in the middle of the night (1 Samuel 3:1, 3, 10–12). It must not have been an easy one to hear. The Lord states He is about to punish Eli's house, meaning him and his descendants to follow, forever. This judgment is God's response to the sin of Eli's sons Hophni and Phinehas. It's also a condemnation of Eli's passive, permissive attitude towards his sons' abusive behaviors. Those sins were detailed in the previous chapter. Hophni and Phinehas abused their power as priests over Israel to serve their appetites. They demanded the best cuts of meat from the sacrifices of the people before they were offered to the Lord (1 Samuel 2:12–17), and they had sex with the women serving outside of the tent of meeting (1 Samuel 2:22).

And yet, the Lord's judgment, is phrased as falling on their father, Eli. The Lord says Eli knew his sons were blaspheming God, and failed to restrain them (1 Samuel 2:22–25). As the high priest of Israel, Eli's sons were under his authority as lower priests. His duty, once he knew about their blasphemy before God by their corruption, was to remove them from office. Eli failed to do that, so in practice he gave greater honor to his sons than He did to the Lord (1 Samuel 2:29).

Eli's sin against the Lord went beyond failing to discipline his sons. Because of their positions as leaders in the nation, his greater sin was to fail to uphold God's holiness before the people. Eli also allowed his sons to sin against the people and to disrupt their worship of God (1 Samuel 2:16–17, 22). When Jesus cleared the temple, He seems to have done so in response to similar sins (John 2:13–17; Mark 11:11, 15–17).