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Mould and Mildew Inside Eavestroughs: A Cleaning and Prevention Guide for Ontario
Eavestrough Cleaning

Mould and Mildew Inside Eavestroughs: A Cleaning and Prevention Guide for Ontario

By Devon Moore August 27, 2025 4 min read

Mould and mildew inside an eavestrough are a symptom, not the problem. Damp debris and slow drainage feed them, so this guide covers how to clean the growth safely and how to fix the conditions that let it take hold.

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In This Article
  1. What is actually growing in there
  2. Protect yourself and the finish first
  3. Cleaning the trough, step by step
  4. Stopping the regrowth
  5. When mould points to a bigger problem

What is actually growing in there

Mould and mildew need three things: moisture, something to eat and time. A trough full of rotting leaves, seed pods and roof grit supplies all three. In Southern Ontario the humid stretch of July and August speeds things up, and a mat of wet leaves left from November has spent the whole winter turning into compost.

You may see black, green or grey patches, a white fuzz, or a slimy film with a musty smell. Algae and slime often grow alongside mould, and you cannot reliably tell them apart by eye, so treat all of it the same way. Growth usually starts where water lingers: low spots, shaded runs on the north side, and the stretch just before a partly blocked outlet.

Dark stripes on the outside face of the trough are a different problem, covered in our guide to black streaks on gutters.

Protect yourself and the finish first

  • Gear. Wear waterproof gloves, eye protection and a dust mask or N95-type respirator. Dried, mouldy debris throws off fine particles when disturbed, and people with asthma or allergies should skip this job.
  • Tools. Use a plastic scoop and a soft brush. Wire brushes and scouring pads scratch the finish, and scratches on steel start to rust.
  • Cleaner. A mild detergent or an oxygen-based cleaner, used as the label directs, handles most growth. Sodium hypochlorite products must be diluted, rinsed off and kept away from plants, and they can dull painted metal.
  • Never mix products. Bleach combined with ammonia or acids can release toxic gas.
  • Ladder rules. Keep three points of contact and stay away from wires. Leave second-storey runs to a crew.
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Cleaning the trough, step by step

  1. Take out the bulk, dry. Scoop the damp material into a bucket and bag it. Do not drop it beside the wall, where it keeps rotting against the siding.
  2. Flush with the hose from the high end, and watch where the water slows or pools. Those spots are your drainage faults.
  3. Scrub the growth with the soft brush and your chosen cleaner. Let it sit for the time on the label rather than scrubbing harder.
  4. Rinse well until the water runs clear, and keep the runoff off garden beds.
  5. Check the drainage again. If puddles remain after the flush, cleaning will not hold. The trough is out of slope, and our gutter pitch guide explains how to confirm it.

Choose a dry day, so the metal dries fully and no damp film is left to feed new growth.

Stopping the regrowth

CauseFix
Puddles that linger after rainRe-hang the run to restore its slope toward the downspout
Leaves and seed pods piling upClean after the spring seed drop and again in November
Constant shade and dampnessTrim overhanging branches so sun and air reach the roof edge
A slow or half-blocked downspoutFlush it and clear the elbows
Heavy debris every yearConsider guards, and still check them

A quick look after the summer storms, from the ground or with a camera on a pole, helps too. If water is standing in mid-July, growth is already under way.

Request a home-service quoteDescribe the work before choosing a date or service scope.

When mould points to a bigger problem

Growth inside a trough rarely gets into the house directly. What matters is why the trough stays wet. Persistent standing water can soak the fascia and soffit, and rot behind them lets water reach the attic edge.

Take it seriously if growth spreads to the fascia or soffit, if the wood feels soft, or if you notice a musty smell or stains upstairs. Mould that has reached siding is a job for algae and mould removal from siding.

D&D Home Services cleans and flushes eavestroughs in Kitchener, Waterloo, Cambridge and Guelph, and it is worth calling a crew for tall or heavily overgrown runs. See gutter cleaning for details. Quotes are free and confirmed in writing.

Key Takeaways

  • Mould and mildew grow where damp debris and slow drainage meet, so cleaning without fixing drainage will not last.
  • Wear gloves, eye protection and a mask, use soft tools, follow cleaner labels and never mix bleach with other products.
  • Puddles that remain after a flush mean the trough is out of slope.
  • Growth on the fascia or soffit, soft wood or a musty smell inside points to a bigger moisture problem.
D&D Home Services
Devon Moore, Operations Lead Co-Founder & Operations Lead, D&D Home Services

Devon Moore is the co-founder and Operations Lead at D&D Home Services, with hands-on experience cleaning hundreds of homes across Kitchener-Waterloo, Cambridge, and Guelph.

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