The most significant lasting effect of Reconstruction was that the issues of racial equality and civil rights were effectively ignored at the national level for the better part of a century. Although Reconstruction was ostensibly concerned with these issues, it lacked the sustained political energy required to make a positive lasting impact on the lives of African Americans.
The changes that took place during Reconstruction were broad, rather than deep. African Americans in the Southern states were allowed to vote and run for public office, but the underlying racial prejudice against them remained; if anything, it was even stronger than it had been before the Civil War. Even the most ardent supporters of Reconstruction didn't believe in racial equality; their attitudes towards race were disturbingly similar to those harbored by the vast majority of Southern whites.
As Reconstruction was a political measure which did not address the underlying issues, it was completely reliant on sustained commitment from policy-makers in Washington. Inevitably, this proved to be an inadequate foundation for Reconstruction. Over time, interest in the policy waned in the Northern states; people were tired of the issue and wanted to move on; and to put the matter bluntly, there were no votes in it for either party.
Gradually, then, African Americans in the South were abandoned to white supremacist state legislatures, who set about re-introducing the substance of slavery through the back door, by way of the segregationist Jim Crow laws. The actions of Southern governors and legislatures were matched at the Federal level by the indifference of senators, congressmen, and Supreme Court justices. The systemic injustice and repression that arose from this toxic combination festered on for the next hundred years or so, until with the Supreme Court, in the case of Brown v Board of Education (1954), and the US Congress, which passed the Civil Rights Act of 1964, the Federal authorities finally began fulfilling the promise the Reconstruction project begun, but never fully completed, almost a century before.