How to Fix Roof Ponding on a Rubber Roof (DIY Leveling Compound Method)

If you have a flat or low-slope roof, you’ve probably noticed puddles that don’t go away for days after rain. That’s called ponding water, and it’s a common issue for older rubber roofs. It shortens the life of your roofing membrane, loosens coatings, and can eventually lead to leaks.

The good news is you can fix it yourself. This blog walks through how to repair low spots using a roof-leveling compound — a lightweight mix you apply directly to the surface to even out dips and help water drain off. It’s straightforward, inexpensive, and easy to do in a weekend.

Why Ponding Water Is a Problem

Ponding happens when water doesn’t drain and collects in dips. Over time, this can:

• Weaken or bubble the roof membrane

• Loosen coatings or sealants

• Add weight that strains the roof deck

• Encourage algae, mold, and dirt buildup

Even shallow puddles will damage the coating if they sit for more than 48 hours. Fixing those low spots now prevents major roof repairs later.

Step 1: Clean the Roof Thoroughly

Start by washing the roof well. Dirt and old coating residue will keep new materials from bonding properly.

1. Power wash the roof.Use an electric or gas pressure washer. Focus on the areas where water collects — they tend to be the dirtiest.

2. Remove flaking paint or coating.Scrape or brush any loose aluminum or elastomeric coating from the surface.

3. Let the roof dry overnight. You want it completely dry before applying anything new. Moisture trapped under the compound will prevent it from curing correctly.

Step 2: Mark the Ponding Areas

Once the surface is clean and dry, identify where the dips are. You’ll usually see them outlined by dust, leaves, or dark stains. Mark those areas with chalk so you know where to apply the compound later.

Step 3: Use a Roof-Leveling Compound

A roof-leveling compound (sometimes called a slope-building compound) is a lightweight mix used to fill low areas on flat roofs. It combines rubber granules, foam beads, and a polyurethane binder that cures into a dense, flexible surface.

Once it sets, it looks and feels similar to playground or running track material — solid underfoot but slightly cushioned. It withstands weather changes and can be coated over once cured. These compounds can be applied on top of your existing membrane or, in large repairs, under a new membrane. For simple ponding repairs, applying it above your current roof is easiest.

Step 4: Gather Materials and Tools

Here’s what you’ll need for the job:

Materials

• Roof-leveling compound

• Polyurethane adhesive or primer

• Oil-based polyurethane (optional backup sealer)

• Silicone or elastomeric roof coating (for topcoat)

Tools

• Power washer

• Mixing pail or heavy-duty plastic bag

• Trowel or steel finishing float

• Straight edge or long piece of wood

• Paint brush or chip brush

• Roller with ½-inch nap

• Utility knife or scissors

• Gloves

Step 5: Mix the Compound

Follow the directions that come with your leveling compound, but generally the process goes like this:

1. Prime the surface.Brush a thin layer of polyurethane adhesive or primer onto the area you’ll fill.

2. Combine the components.Add the compound base and the adhesive into a sturdy mixing bag or bucket.

3. Mix by hand.Push the bag side to side or stir until the material blends evenly. It should feel slightly sticky, with no dry clumps or patches.

4. Work in small batches.Only mix as much as you can spread within 10–15 minutes.

Step 6: Apply the Leveling Compound

Pour the mixed compound directly into the low section of the roof. Use your trowel to press and spread it evenly.

• Start at the deepest part of the dip and feather outward.

• Keep the material about 1 inch thick at the center, tapering to zero at the edges.

• Use your straight edge or a long board to drag across the surface so it blends smoothly into the surrounding roof.

The compound is lightweight and easy to shape, so take your time smoothing it out. It should look like a gentle ramp rather than a mound.

Step 7: Work in Sections

Do one ponding area at a time. For each section:

1. Brush on primer adhesive.

2. Pour and spread the compound.

3. Level it with your trowel and straight edge.

Make sure your gloves stay clean — once the binder starts curing, it can get sticky fast.

Step 8: Mix Thoroughly and Evenly

A common mistake is not stirring the material deep enough. If you don’t mix thoroughly, the foam beads may stay at the bottom and make the patch look pale or uneven.

If that happens, don’t worry — it’s mostly cosmetic. But for a solid bond, try to keep the mix uniform before pouring. If loose beads end up on the roof after curing, just vacuum them up once dry.

Step 9: Allow to Cure

Let the compound cure for at least six hours before applying any topcoat. The time can vary with temperature and humidity. It should feel firm but slightly springy under light pressure. If you see soft or crumbly spots, they may need a second layer or reinforcement with adhesive.

Step 10: Reinforce Loose Spots

If any sections feel too soft or lift up when you touch them, you can re-bond them easily.

Brush on a thin layer of oil-based polyurethane over the loose area and let it soak in. It will harden and stabilize the patch. This is a quick alternative if you run out of the original adhesive or need to touch up on short notice.

Step 11: Add a Reflective Roof Coating

Once your patch is firm and dry, apply a silicone or elastomeric roof coating to protect it. This seals the surface, reflects UV rays, and helps keep your roof cooler.

How to Apply the Coating

1. Brush the edges.Use a chip brush to cut in around seams, vents, and flashing.

2. Roll the main surface.Pour a small amount of coating onto the roof and spread with a roller. Work in sections for even coverage.

3. Apply thin layers. It’s better to roll two light coats than one thick one.

If pieces of the cured compound stick to your roller, just remove them and keep going — they won’t affect the finish.

Step 12: Let It Dry Overnight

Allow the coating to dry fully before walking on it. By the next morning, it should have a smooth, bright finish. Check the repaired areas for small bubbles or lifting edges. If you see any, cut them off and apply another thin layer of coating or sealer.

Step 13: Final Inspection

After drying, look over the roof carefully:

• The filled sections should blend smoothly into the surrounding surface.

• The coating should be even and fully sealed.

• There should be no soft spots or exposed filler.

The new slope will guide rainwater off instead of letting it sit in puddles.

Step 14: Test After the Next Rain

When it rains again, go up after the storm and check your work. You’ll probably see a small amount of moisture where it used to pond, but it should drain quickly and dry within a few hours. A little bit of shallow water immediately after rainfall is normal — what matters is that it doesn’t linger.

Step 15: Maintain Your Roof Regularly

Even with proper drainage, flat roofs need regular maintenance. Every few months:

• Remove leaves, sticks, and debris from the surface and gutters.

• Check for cracks or lifted seams in the coating.

• Reapply a thin coat of silicone or elastomeric sealant every couple of years.

This keeps the roof bright, reflective, and watertight.

Extra Tips for DIY Roof Ponding Repairs

• Always work on a dry day. Humidity slows down curing time.

• Wear gloves and long sleeves. The compound and sealant are sticky until cured.

• Don’t skip the primer. It’s what makes the compound adhere to rubber, asphalt, or metal surfaces.

• Keep your slope subtle. You only need enough pitch for water to move, not a steep incline.

• Avoid using too much product. Thick patches can crack; thin layers blend better and cure stronger.

What If You Still See Ponding?

If the water still pools after repairs, it may be due to:

• A larger structural dip in the roof deck

• Blocked drains or scuppers

• Sagging insulation beneath the membrane

You can add a second layer of leveling compound or create a wider sloped section to help water move toward the drain. If that doesn’t fix it, you might need to remove sections of old roofing and rebuild the slope from the deck up — a job best handled by a professional roofer.

Benefits of Fixing Ponding with a Leveling Compound

This method is ideal for homeowners because it’s:

• Cost-effective. No need to re-roof the entire area.

• Lightweight. Won’t overload the roof structure.

• Durable. Withstands sun, rain, and foot traffic.

• Eco-friendly. Many compounds use recycled materials.

• Simple. No special equipment needed beyond basic tools.

The end result is a smoother, more efficient roof surface that drains quickly after rain.

Final Look and Results

Once finished, your repaired roof will have:

• A bright, reflective coating that reduces heat buildup

• A smoother slope where water once collected

• A seamless finish ready for all weather

After heavy rain, any leftover water should dry within a day — no deep puddles, no soft spots, and no leaks.

Conclusion

Fixing roof ponding doesn’t have to mean tearing off your roof or spending thousands. By using a lightweight leveling compound and protective silicone coating, you can eliminate standing water, extend your roof’s life, and improve energy efficiency — all in a weekend.

Take your time cleaning, mixing, and smoothing, and your roof will drain like new again.