TL;DR
The black spots under a rubber bath mat are mildew growing in a thin layer of trapped water that never sees air. Scrub the mat with a brush and a cleaner suited to the material, pay particular attention to the suction cups, and rinse it thoroughly. Then change the habit: lift and hang the mat after every use, because a mat left flat will grow it all back within days.
Why the underside is always the worst part
A suction cup mat works by sealing to the tub floor. That seal is exactly the problem.
Water gets under the mat, either during a bath or from splashing, and then it cannot evaporate because the mat is sitting on top of it. What is left is a thin, permanently damp film in complete darkness with soap residue and skin cells for food.
Mildew grows there in days. Each suction cup is a small cup holding its own reservoir, which is why the spots are worst in a ring pattern that matches the cups.
The tub surface underneath discolors too. Soap scum and body oil bond to the tub in that film, and a mat left in place for months can leave a permanent stained outline.
The same trapped-water problem explains the black gunk in squirting bath toys, covered in how to clean bath toys that squirt black gunk.
How do you clean a rubber bath mat?
Lift the mat, lay it face down in the tub, and scrub both sides and every suction cup with a stiff brush. Use a paste of baking soda and water for light buildup, or a diluted bleach solution for set-in mildew stains, then rinse very thoroughly and hang the mat to dry completely.
The scrub, step by step
1. Take the mat out and check for a care label. Many mats are machine washable, and the label decides.
2. Rinse both sides with hot water. This softens the soap film that binds everything else.
3. Scrub with a stiff brush. Both sides, and pay real attention to the suction cups. A small brush or an old toothbrush gets inside each cup where a big brush skates over.
4. Use a baking soda paste for light buildup. Sprinkle baking soda over the wet mat, work it with a brush, and let it sit ten minutes before scrubbing. It is mildly abrasive, safe on rubber and vinyl, and involves nothing hazardous.
5. Use a diluted bleach solution for set mildew. Roughly half a cup of household bleach per gallon of water, applied to the mat, left for five to ten minutes, then rinsed very thoroughly. Run the exhaust fan and open a window.
6. Rinse until no cleaner remains. Residue makes rubber slippery, which defeats the entire purpose of a non-slip mat.
7. Hang it to dry fully. Over the tub edge, a shower rod, or a towel bar. Both sides exposed to air.
Two hard rules on bleach. Never mix it with vinegar or any acid, which releases chlorine gas. Never mix it with ammonia, which is in some glass cleaners, and never with rubbing alcohol. Use one product, rinse completely, and ventilate.
Machine washing, if the label allows it
Many rubber and vinyl mats can go in a washing machine, and it is an easy way to handle a badly neglected one.
Put the mat in with two or three old towels, which provide the scrubbing action and stop the mat from slapping around the drum. Use warm water and a normal detergent dose, plus half a cup of baking soda for odor. Do not use hot water, which warps rubber and destroys suction cups.
Never put a bath mat in a dryer. Heat degrades rubber and vinyl, cracks suction cups, and can damage the machine. Hang it to dry instead. This is the same reason drying discipline runs through cleaning the personal items you use every day.
Why do suction cups stop sticking?
Suction cups fail when soap film, body oil, or mineral scale coats either the cup or the tub surface, because suction needs a clean, smooth, wet seal. Scrub each cup with a small brush and a degreasing dish soap, clean the tub floor properly, wet both surfaces, and press the mat down firmly.
Getting suction back
Clean both halves of the seal -- a spotless mat on a greasy tub still will not stick. Wash the tub floor with a degreasing cleaner rather than a general spray, since body oil and conditioner residue are what break the seal.
For mineral scale on the cups, a soak in one part white vinegar to three parts warm water for thirty minutes dissolves it. Rinse thoroughly afterward and do not combine it with anything else.
Wet both the mat and the tub before positioning it, then press each cup down firmly with your thumb. If cups are cracked, hardened, or torn, no cleaning will help.
Fabric-backed and other mat types
Not every bath mat is rubber, and the method changes.
Vinyl and PVC mats clean like rubber but are less heat tolerant. Warm water only, and no bleach on printed designs, which fade.
Fabric-backed mats with a rubber or latex non-slip layer should be washed cool and air dried. Heat crumbles the backing, which is why old mats leave rubber crumbs everywhere.
Wooden, teak, and bamboo mats must never be soaked. Wipe, scrub with a brush and soapy water, rinse quickly, dry standing on edge, and oil them occasionally.
Silicone mats are the easiest. Nonporous, dishwasher safe on many models, and they dry fast.
Replacing it, and preventing the problem
Replace a mat when the suction cups are cracked or hardened, when the surface has gone slick, when mildew stains will not come out, or when the material is stiff and cracking. A mat that has stopped gripping is a fall risk, and that outranks any cleaning question.
Prevention is simpler than any of the above. Lift and hang the mat after every single use -- this one habit eliminates most of the problem. Run the exhaust fan during showers and for fifteen to twenty minutes after, and wipe the tub floor so water is not sitting there.
Wash the mat weekly rather than monthly. A short scrub every week beats a long fight every season.
Keep items off the tub floor generally, which is also what stops the slime described in how to clean a soap dish that stays slimy and the corrosion in how to clean a shower caddy and stop rust rings.
Source: U.S. Environmental Protection Agency guidance on controlling moisture and mold in the home
FAQ
How do you get black mildew off a rubber bath mat?
Lay the mat face down, scrub both sides and every suction cup with a stiff brush, then apply a diluted bleach solution of about half a cup per gallon of water and leave it five to ten minutes before rinsing very thoroughly. Ventilate the room and never mix bleach with any other cleaner.
Can you put a rubber bath mat in the washing machine?
Usually yes, if the care label allows it. Wash it with two or three old towels on a warm cycle with normal detergent. Do not use hot water, which warps rubber and ruins suction cups, and never put a bath mat in the dryer, since heat cracks and degrades the material.
Why does my bath mat suction cups stop sticking?
Because soap film, body oil, or mineral scale coats the cups or the tub surface, and suction needs a clean smooth seal on both sides. Scrub the cups with a small brush and degreasing dish soap, wash the tub floor, wet both surfaces, then press each cup down firmly.
How often should you clean a bath mat?
Weekly for a mat in daily use, with a rinse and a hang after every use in between. A weekly scrub keeps mildew from ever establishing, which is far easier than removing set-in black staining later. Mats used less often can go two to three weeks.
Can you use vinegar on a rubber bath mat?
Yes, a solution of one part white vinegar to three parts warm water dissolves mineral scale on suction cups and helps with light soap film. Rinse thoroughly afterward. Never use vinegar in the same session as bleach or mix the two, since combining them releases chlorine gas.
When should you replace a bath mat?
Replace it when suction cups are cracked or hardened, when the top surface has gone slick, when mildew staining will not scrub out, or when the material is stiff and crumbling. A mat that no longer grips is a fall hazard, and that matters more than how it looks.
Mats are a weekly job. A bathroom that is genuinely clean top to bottom is a bigger one. If you would rather hand that off, get a quote or read more about house cleaning services.