How can I waterproof rope-covered outdoor planters?

Sisal or Manila rope. You can even use polypropylene rope. E6000 to glue it on. Hot glue won't last. I know! You can use spray water based polyurethane to seal natural rope. Look in the rope department and see what appeals to you.

Hemp and wood glue- Use a throw away plastic cup. Cover surface where you are working. Pour the yellow wood glue into the cup. Dip the rope in the glue and start winding. After it is finished allow to fully dry 30 hours. You can paint over this to change the color or clear gloss

THis type of rope should work fine: https://amzn.to/2IPZdzq

All rope will rot but nylon will last the longest but probably not the look you were going for.

Funny, I'm actually doing a large one now but ran out of rope. I'll attach a pic. cause I think it'll help.

I don't know about it being "the best" overall exterior adhesive but on a project like this, 100% clear silicone outdoor adhesive caulk for windows & doors is probably the best choice (GE Silicone II). It's flexible, weatherproof, mold-proof & UV stable so it won't yellow. I used a little super glue on the rope ends to keep them from fraying, as well as a dab every couple inches on the first row to keep the rope stable & level. Silicone cures pretty fast but it's not stable until it's fully cured. I also used a piece of painters tape to keep the newly applied rope in place to prevent the weight of the remaining rope from pulling it down, in between rows or when I took a break. Just start from the bottom, work up & keep it clean because you cannot paint 100% silicone.

As for sealing or just preventing mold on natural fibers, you do have options. I have parrots & use untreated natural rope outdoors. Mold can be cleaned & killed with a solution of white vinegar & non concentrated Dawn dish soap. So you don't have to treat it at all. However, untreated rope will eventually breakdown.

To seal natural fibers rope, rugs... you need to use either latex paint or acrylic paint for exterior use. All of which are available in clear. Some of the best non yellowing exterior sealers/varnishes are found at craft & marine stores. If you use colored paint, I think applying a protective clear coat over that would be a good idea, to prevent it from wearing down.

On a side note, I just recently treated my outdoor cushions as well as the convertible top on my daughter's car. I used the brand 303 (can purchase on Amazon or at some auto parts & marine stores). So I do know this stuff works. HOWEVER, I have not tried using it for this particular application. So I don't know if the treatment will compromise the silicone adhesion. But a small test run wouldn't hurt. Anyway, if you want to keep the rope soft, you can try to give it a good soaking with 303 tonneau cover/soft top/canvas/bimini top waterproofing spray. It smells bad so it has to be applied outdoors. Clean brand new rope will need 2 treatments at first. You will also need to retreat every 12-24 months depending on your location.

Over a year ago I did try Rustoleum 'Never Wet' on my exterior rope macrame plant hanger. It left a cloudy rubber-like coating I don't care for (pic). Although it wasn't a deal breaker for what I was using it for & has held up to the south Florida climate, I wouldn't choose to purchase it again.

Hope ALL this info helps.