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What Happens If Ponding Water Is Left on a Flat Roof? 

If you’ve noticed puddles forming on your flat roof after a rainstorm (aka “ponding water”), it’s natural to wonder, “Are puddles on my flat roof a problem?” The short answer is: yes—especially if that water sticks around.

At Weather Shield Roofing Systems™, we’ve spent over 40 years helping commercial property owners and managers protect their buildings from water damage. We’ve seen how fast a small puddle can lead to big trouble.

Let’s break down why water pools on flat roofs, what happens when it stays too long, and how to fix it.

Should Water Ever Create Puddles on a Flat Roof?

Technically, flat roofs aren’t completely flat—they’re designed with a slight slope to help water drain off the surface. That said, it’s not unusual for water to take a little time to clear off after a storm. But if water is still puddling 48 hours after the rain stops, that’s a red flag.

These puddles, also known as ponding water, signal that your roof drainage system—including your roof drains, scuppers, or gutters—isn’t working as it should. And when water doesn’t drain, it starts to cause real damage.

What Happens If Ponding Water Is Left Alone?

•  It Deteriorates Your Roofing System: Commercial roofs can handle a lot—but not puddles that linger. Whether your roof has TPO, EPDM, or modified bitumen, standing water wears it down faster. Moisture breaks down adhesives, weakens seams, and softens the insulation underneath. Imagine a sponge soaking in water too long—it falls apart from the inside out.
• It Leads to Costly Leaks: When roofing materials weaken, leaks start. All it takes is one small hole or a loose seam, and water slips inside. Leaks often go unnoticed at first. Water can soak insulation, grow mold, and damage walls or ceiling tiles before you ever see a drip. What could’ve been a quick fix can turn into a major repair job.
• It Adds Dangerous Weight to Your Roof: This surprises a lot of building owners: one inch of water spread over a 10×10 area weighs over 500 pounds. Multiply that across your whole roof, and you could have thousands of extra pounds sitting on it. Roofs aren’t built to carry that weight long-term. It causes sagging, creates more low spots, and leads to even more ponding. In extreme cases, it can cause structural damage.
• It Grows Mold, Algae, and Vegetation: Ponding water acts like a shallow pond—it attracts dirt, debris, and eventually, growth. Algae, mildew, and moss can start to grow in and around the puddles, damaging your roofing membrane further. These organisms break down your roof membrane and block drains. Worse, mold can affect the health of the people inside your building.
• It Can Void Your Warranty: Many commercial roof warranties come with specific conditions, and one of the biggest is proper drainage. If your manufacturer sees that ponding water caused the damage, they may not cover the repair costs.

How Long Can Ponding Water Sit on a Flat Roof Before It’s a Problem?

If water hasn’t drained 48 hours after a storm, it’s considered ponding. That’s when it becomes a serious issue. It’s not just cosmetic—it points to a design or drainage problem. And the longer it stays, the more damage it does.

How Do You Stop Ponding Water on a Flat Roof?

Great question—and one we get asked all the time. Here are some proven steps:

Clear and Maintain Roof Drains: Clogged drains are a top cause of ponding. Clean out leaves, trash, or debris often. Make sure your scuppers and gutters are clear too.

Inspect for Low Spots: Settling or compressed insulation can cause dips in the roof. Water then collects there. You can often fix this with tapered insulation or added material to reshape the slope.

Check Slope and Design: Your roof should have at least a slight slope (usually ¼ inch per foot) toward drains or edges. If that slope has shifted over time, water can’t flow off like it should. A roof inspection can catch this.

Add or Upgrade Roof Drains: In many cases, the best fix is installing additional roof drains or scuppers. Extra drains or scuppers can pull water away from problem areas. If your building has changed over time—maybe an addition or heavier equipment—your old drainage system might not cut it anymore.

Routine Roof Inspections: Regular inspections can catch small problems before they grow. At Weather Shield Roofing Systems, we offer detailed inspections as part of our Max Life Roof Care program to catch these problems early—and fix them cost-effectively.

Should You Be Worried About Those Puddles?

If you’re wondering, “Are puddles on my flat roof a problem?” or “How do I stop standing water before it causes damage?”—you’re asking the right questions.

Even small puddles can lead to big repair costs if you ignore them. The good news? Most drainage issues are fixable if you act early.

At Weather Shield Roofing Systems™, we help commercial property owners and managers solve ponding problems and extend their roof’s lifespan. Whether you’ve got standing water now or just want peace of mind, we’re here to help you make smart, cost-effective choices.

Let’s make sure those puddles don’t turn into problems. Reach out anytime—we’re always happy to talk through your options.