Atlanta’s price hikes in real estate slowed as summer began, according to the latest data from the closely watched Case-Shiller Home Price Index.

But even after two years of those increases, metro Atlanta leads the nation in the percentage of homeowners who are “under water,” that is who still owe more on their mortgages than their houses are worth, according to a separate study.

Atlanta’s average prices were up 1 percent in June from May and up 8.6 percent compared to the same period of a year ago, Case-Shiller reported this morning. That nearly matched the results of the nation’s top 20 markets – 1 percent in the month and 8.1 percent over the year.

More than five years after the official end of the recession, Atlanta’s residential real estate market is still recovering.

Atlanta’s average home prices have come a long way since hitting bottom in March of 2012: the average price since then is up 43.6 percent. And in some areas, they may very well be above those previous peaks.

But in some places, the market has been weak and even where there’s a rebound, the market in many neighborhoods was slow to gather speed. On average, Atlanta prices are roughly 12.4 percent below their peak, which was reached in August of 2006.

As a result, the proportion of metro Atlanta homeowners who are “under water” has improved in the past year from 44 percent to 28.9 percent, according to Zillow, a national real estate research company

Yet that still leaves Atlanta with the worst proportion of owners with “negative equity,” albeit only slightly worse than Las Vegas, according to Zillow.

The national average is 17 percent.