Across the U.S. today, over 15% of homeowners owe more on their mortgage than what their home is actually worth. The real estate bubble burst over seven years ago, yet this fact is just the tip of the iceberg of how the so-called housing recovery has left many Americans behind.

Last month, real estate website Zillow.com released its quarterly Negative Equity report for the first quarter of 2015. The report finds that while the percentage of homes with negative equity -- when the mortgage is greater than the value of the house -- is half what it was at its peak in 2012, tremendous challenges remain.

A nationwide problem with a local twist
According to Zillow.com's report, there are 7.9 million underwater mortgages in the U.S. today. Of those, 52% are underwater by more than 20%.

Zillow economists predict home prices will appreciate by approximately 2% per year for the foreseeable future, meaning it will take at least through 2020, if not longer, for those nearly 4 million homeowners to reach the break-even point between their mortgage and home value.

The problem exists from coast to coast, but that doesn't mean it's evenly distributed. Hot economies, predictably, have a far lower rate of underwater mortgages than locales with struggling economies. 

Just 6.1% of mortgages in San Francisco, for example, are underwater. San Jose has the lowest rate in the nation, at just 3.8%. Austin, Texas; Houston, Texas; and Denver, Colorado all also report much better than average figures. 

On the other side of the coin, three of the top five highest percent metros are in the Midwest: Chicago at 23.7%, St. Louis at 20.4%, and Cleveland at 19.9%. 

Disproportionately bad for the poor
Digging into the numbers in the report a little deeper, it becomes clear that lower-income households are bearing the brunt of the slow recovery far more so than their wealthy counterparts. Zillow found that homes valued in the bottom one third of the market are three times more likely to be underwater that the highest-valued third.

Detroit is an excellent example of this phenomena. The city's bottom one third of housing, by value, has a huge negative equity rate of 46%. That compares with a 7% rate for the upper third. Likewise in Atlanta, where the bottom third also has a 46% rate versus just 10% for the upper third.

For the U.S. as a whole, 25% of the bottom tier of homes are underwater, compared to 8% for the top tier. 

Real economic consequences
For investors and the broader economy, this reality is a serious problem.

With the appreciation of home prices moving relatively slowly, it will take years for underwater homeowners to have enough value to break even on their homes. Worse yet, when you take into consideration the costs of selling your home -- sales commission, taxes, and so on -- home prices will have to rise between 30% and 40% just to realize any cash benefit to selling a home after expenses.

For existing homeowners, that means waiting years before home prices reach levels high enough to sell for a profit and buy a new home, or they must face the prospect of a foreclosure or a short sale to get out from underneath the mortgage.

It's also a big problem for current and future first-time home buyers because such a large percentage of lower-priced homes will be locked up for years to come as those existing homeowners wait to sell.

That will almost certainly dampen the housing market over the next decade, not to mention the pressure it puts on the banks that must then take losses on these loans in either a short sale or foreclosure situation.

Does this mean investors should avoid real estate altogether? No, I don't think so. However, investors shouldn't expect real estate and real estate related industries to fully recover anytime soon. The housing market may be recovering, but it is a long way from being completely healed.

Jay Jenkins has no position in any stocks mentioned. The Motley Fool recommends Zillow. The Motley Fool owns shares of Zillow. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.