How to Fix Standing Water on a Flat Roof

If you’ve ever had standing water on your flat roof, you already know how frustrating it is. Puddles can turn into leaks, cause rot, and lead to bigger structural problems. The good news? You can fix it yourself.

In this blog, we’ll walk through how to remove standing water and install a giant roof scupper—a drainage opening that lets water flow off your roof properly. This project comes straight from a real repair job, so you’ll see every part of the process, from prep to finish.

Why Standing Water Is a Problem

Standing water (also called “ponding water”) happens when rainwater or melted snow doesn’t drain off your flat roof. Over time, it can:

• Weaken roofing materials

• Cause leaks and rot

• Add unnecessary weight to your roof structure

• Lead to mold and insulation damage

Even a small puddle can become a serious issue if ignored. That’s why it’s important to deal with it early.

The Plan: Install a Scupper

The fix here is a scupper, which is basically an opening on the edge of the roof that allows water to drain through. It’s lower than the rest of the roof so water naturally flows out.

We’ll install a four-foot-wide scupper—large enough to handle heavy rain. Before diving into tools and steps, let’s take a look at what we’re dealing with.

Assessing the Roof

Before starting, take a walk around your roof. In this project, there were two roofs side by side. One had a bit of standing water—no big deal. The other had a serious problem. That’s where the scupper needed to go.

Check your roof for:

• Large puddles that don’t dry after 48 hours

• Areas that sag or dip

• Blocked drains or low-spots near parapet walls

Once you’ve identified the problem area, you can begin prepping the site.

Step 1: Prepare the Roof

Start by removing as much standing water as you can. You can use a push broom, wet vac, or mop to get rid of the puddles. It’s a messy job—you might get your legs wet. That’s part of the process.

After clearing the water, clean the roof surface thoroughly. This helps new materials stick properly later on.

Step 2: Clean the Work Area

Once the water is gone, clean the surface where you’ll work. Use a roof membrane cleaner—specifically something like JM Weathered Membrane Cleaner.

This cleaner removes mud, oil, and residue so that adhesives and seam tapes can actually bond. You don’t need to scrub the entire roof—just focus on the section where you’ll be cutting and installing.

Step 3: Cut the Roof

Now it’s time to cut into the roof.

Carefully mark the area where you’ll install the scupper. Use a utility knife or a roofing knife to slice through the top membrane layer. In most cases, that’s EPDM roofing (a rubber-like layer).

After cutting, remove the separator board (often made of fiberboard) underneath. You’ll see screws and plates holding it down—unscrew and remove them.

Step 4: Remove Old Roofing Layers

This roof had several layers, and that’s more common than you’d think. Here’s what we found during the cut:

• Top layer: EPDM roofing

• Below that: Built-up roofing (asphalt and felt)

• Then a perlite board

• Another built-up layer

• And finally plywood underneath

That’s three roofs stacked together—way more than the recommended maximum of two. The only way to do this right is to remove all those layers until you reach the wood decking.

Step 5: Inspect What’s Underneath

Once the old roofing layers are gone, inspect what’s underneath. You might find surprises—like shingles or bent plywood—which should never be part of a flat roof assembly.

In this particular case, the roof had a very unusual setup:

• The framing and brickwork were done well.

• But the bricks and mortar were set too high.

• Instead of fixing that, someone added half-inch plywood layers on top and bent them upward against the brick wall.

That’s not how roofs are built. Those plywood layers don’t connect to rafters or form a proper curb. It’s a patch job, and it traps water instead of letting it drain. So, we removed all that excess plywood to rebuild the section correctly.

Step 6: Identify the Rafters

Next, find your rafters (the structural wood beams below the deck). You’ll need to know where they are before cutting or attaching new materials. Cut a small inspection hole and look for nails or screw lines—those usually indicate where the rafters run. Mark them with a line using a chalk line or marker. That’s where you’ll anchor new wood later.

Step 7: Cut and Lower the Roof Edge

Now that you know where the structure sits, it’s time to lower the roof edge where the scupper will go. Cut through the fascia (the vertical board at the roof edge), and into the gutter area. You’ll also remove a few bricks if they’re too high. The idea is to lower the roof edge so that water naturally flows toward the opening. This is what makes the scupper work—it needs to be slightly below the rest of the roof.

Step 8: Install New Plywood Decking

Once the area is prepped, install a new piece of plywood decking. Cut it to fit snugly into the lowered section you just made. Screw it down using GRK 9x2½-inch screws (or any quality construction screws). GRK is a favorite among many roofers for its strength and reliability. Make sure the plywood is flush and level with the surrounding deck but slopes slightly toward the edge.

Step 9: Cut the Fascia and Gutter

After securing the plywood, trim the fascia and cut back the gutter. Since you’ve lowered the section, the gutter lip might now sit too high. Cutting it down ensures water can flow straight out instead of pooling again.

Step 10: Add Tapered Insulation Board

Next, grab a tapered edge board—a piece of fiberboard that’s thick on one end and gradually thins out. This creates a gentle slope to direct water from the back of the scupper toward the front.

Place it in the lowered area, check the fit, and fasten it down using plates and screws. This step is crucial because it ensures proper drainage and prevents future ponding.

Step 11: Apply Primer and Cover Tape

Now you can start waterproofing.

1. Prime the area using a single-ply low VOC primer. This helps the tape stick to the membrane surface.

2. Apply five-inch cover tape along the seams to seal everything in.

3. Press it down firmly with a roller to remove air bubbles.

Cover taping the seams keeps water from sneaking underneath the new roofing layer.

Step 12: Install the EPDM Membrane

Once the surface is primed and the board is in place, roll out your new EPDM membrane. Cut it to size, glue it down, and make sure the seams overlap properly. The cleaner and smoother the surface, the better the bond. Pay close attention to the corners and edges around the scupper—these are common leak points.

Step 13: Seal All Seams

After taping and gluing, it’s time for the final seal. Use a high-quality roofing caulk around:

• The perimeter of the scupper

• All seams and overlaps

• Any areas where two materials meet

This creates a watertight seal that protects your work from heavy rain.

Step 14: Check the Weather and Finish Up

Roof work depends on weather, so check the forecast before starting. In this project, rain was coming within the hour, so time was tight.

Once you’ve sealed everything, take a few minutes to inspect your work:

• No visible gaps or bubbles

• Seams pressed tight

• Proper slope toward the scupper

When everything looks good, you’re done. The roof is ready for rain.

Results: The Roof Now Drains Naturally

After the repair, water immediately flowed off the roof through the new scupper—no more standing water. That’s exactly what you want. It’s a simple system: water comes down, hits the slope, flows into the scupper, and drains through the gutter. No puddles, no leaks, no more worrying about roof damage.

Materials and Tools Used

Here’s a complete list of what was used during the project:

Materials:

• JM Weathered Membrane Cleaner

• Fiberboard (separator board)

• Plywood (½-inch)

• GRK 9x2½-inch screws

• Plates (for securing fiberboard)

• Tapered insulation board

• EPDM membrane

• Single-ply low VOC primer

• 5-inch cover tape

• Roofing caulk

Tools:

• Utility knife / Roofing knife

• Screw gun or drill

• Chalk line

• Tape measure

• Roller for seam tape

• Brush for primer

• Caulking gun

• Broom or mop (for removing water)

Pro Tips for DIY Roof Drainage

1. Work safely. Always use a harness if your roof has any slope. Even flat roofs can be slippery when wet.

2. Don’t skip cleaning. Adhesives and tapes only stick properly to clean surfaces.

3. Avoid over-layering. If your roof already has two layers, remove the old material before adding new.

4. Check your slope. You need at least a ¼-inch drop per foot for water to flow correctly.

5. Seal everything. Even tiny gaps can cause leaks later.

Common Mistakes to Avoid

• Leaving debris under the membrane. It can puncture the roof from underneath.

• Not priming properly. Tape and glue won’t bond well to dusty or oily surfaces.

• Ignoring the weather. Never work if rain is expected before the adhesive cures.

• Skipping caulk. The final caulking step is what makes everything waterproof.

Maintenance After Installation

After your scupper is installed and sealed, do a quick inspection every few months:

• Clear leaves or debris blocking the scupper opening

• Check seams for cracks or peeling

• Re-apply caulk if it starts to dry out

• Look for any new pooling after a heavy rain

Regular maintenance will keep your flat roof drainage working for years.

Understanding the Layers in a Flat Roof

If you’re new to roofing, it helps to understand the layers you’re dealing with:

1. Top membrane (EPDM, TPO, or PVC) – The waterproof barrier.

2. Insulation board – Keeps your building energy efficient.

3. Cover board (fiberboard or perlite) – Adds rigidity and protects insulation.

4. Roof deck (usually plywood or metal) – The structural base.

When you cut into your roof, knowing what’s what helps you replace materials correctly.

Why There Shouldn’t Be More Than Two Roof Layers

In the example above, there were three full roofs stacked on one building. That’s a major issue.

Each additional layer adds:

• Extra weight

• Reduced flexibility

• More trapped moisture

Building codes usually allow a maximum of two roof systems. If you already have two, the old one must be removed before installing a new one.

What Makes a “Weird” Roof

This roof earned the title of “the weirdest roof in Norwalk” for good reason. The builder tried to fix high bricks and mortar by adding two layers of plywood bent up against the wall.

That kind of shortcut causes:

• Trapped water

• Weak seams

• Poor drainage

• Extra stress on the fascia

If you ever see plywood bent upward like that, remove it and rebuild properly.

Why Scuppers Work So Well

A scupper works by letting gravity do all the work. Instead of pooling in the middle, water finds the lowest point (the scupper opening) and drains through the wall into a downspout or gutter.

They’re especially useful on:

• Flat commercial roofs

• Residential flat roofs

• Parapet walls that trap water

They’re also easy to maintain—just clear leaves and debris occasionally.

When to Call a Professional

This project is doable for an experienced DIYer, but not every roof is safe to work on. Call a professional if:

• You’re unsure about cutting into the roof structure

• There’s electrical or HVAC equipment nearby

• You find more than two existing roof layers

• You notice major structural damage or rot

A licensed roofer can inspect and help you rebuild safely.

Final Inspection Checklist

Before you wrap up, double-check the following:

✅ Scupper opening is at least ½ inch lower than roof surface

✅ All seams are taped and pressed flat

✅ Plywood and insulation are firmly secured

✅ Gutter edge is trimmed so water flows freely

✅ Caulk is applied around every seam and corner

If all that looks good, your roof is ready to handle rain without puddles.

Key Takeaways

• Standing water can ruin a flat roof if ignored.

• Installing a scupper is a practical, long-lasting fix.

• Always remove extra roof layers before rebuilding.

• Clean surfaces and proper sealing are the difference between success and leaks.

• A few hours of careful work can save thousands in roof repairs later.

Final Thoughts

Fixing standing water isn’t glamorous work—you might get soaked, covered in mud, and find a few surprises under your roof layers. But once it’s done, watching rainwater drain away effortlessly is satisfying. With the right tools, patience, and attention to detail, you can solve ponding issues yourself and extend the life of your flat roof.