ep—let’s bake that “real world” planting truth right into the article (because nature does not care how much you paid for that water lily 😄).

The Best Hardy Water Lilies for Natural Earth Bottom Ponds

Winter-hardy perennial water lily varieties for the USA (bigger plants + better blooming)

The best hardy water lilies for natural earth bottom ponds are winter-hardy perennial varieties that make big pads, big flowers, and bloom often. Plant hardy water lilies into firm soil on a sunny embankment in 1–3 feet of water, and protect new plantings from wildlife. Do not plant water lilies in open ponds with carp—carp destroy rooted plants.

How do you plant hardy water lilies in an earth bottom pond?

(No—containers are not required for this.)

Earth bottom ponds are made for direct planting. Pond Megastore notes many plants can be planted directly in the soil on the shelves and bottom of your pond.

Step-by-step: Planting on the embankment (simple + works)

1. Pick the right spot: full sun is best (6+ hours), and calmer water helps lilies thrive.

2. Choose the right depth: plant in 1–3 feet of water where there is earth (not all rocks).

3. Make a planting pocket: scoop a shallow hole into the embankment/soil shelf so the rhizome can sit snug.

4. Set the rhizome correctly: lay the hardy water lily rhizome so the growing tip faces out and or up toward open water and the crown sits near the soil surface (don’t bury the crown in the mud).

5. Firm the soil hard: press soil around it so it can’t float up or wash out. If you have leaves some short leaves will have too much air and may need trimmed to prevent the rhizome from being pulled out. Longer pads on the surface wont pull on the rhizomes as they have reached the surface. 

6. Protect it immediately (this matters): install your temporary fencing before you walk away (details below). Must be like netting / nylon something that is from mud to well above the waterline. 

7. Check often until it grabs: once new roots “lock in,” it becomes much harder to steal or uproot.

Read this before you plant: Wildlife can erase your lilies fast

Pond Megastore already warns that waterfowl, koi/carp, turtles, deer, and other animals will eat water lilies, and recommends fencing until established.
In the wild, lily pads and roots are food, not decorations—deer and rodents can browse them, too.

1) Never plant water lilies in open ponds with larger carp / white amurs

If carp are present (including koi/common carp), your lilies are on borrowed time. Common carp are documented to destroy rooted aquatic plants while feeding/rooting and can wreck plant beds.
Bottom line: If you have carp, either don’t plant lilies in the open—or plan on serious exclusion barriers.

2) Heavy turtle ponds need fencing (minimum 3 months, best = full season) Turtles like water lily stems, often you see leaves floating away from the plants, this is from turtles, they eat the stem and the leaf floats away.  They can do this over and over as the lily sends up more leaves until the lily is so stressed its not sending up leaves. If you have lots of lilies though they can eat a few stems here and there without picking on one lily to the point of no return. 

Pond Megastore notes: “One turtle alone can eat a waterlily in an night or two”
So your plan is simple: assume turtles will try.

3) Deer and nutria are real threats in natural settings

• University sources note white-tailed deer eat water lily leaves and stems, and muskrats/rodents feed on roots and leaves.

• Nutria are well known for heavy herbivory and feeding on roots/rhizomes/tubers, damaging wetland vegetation.

The fence plan (make it part of the planting job)

Here’s the protection standard you asked for—written so customers actually do it:

Minimum protection (recommended for any natural pond)

• Minimum: 3 months of temporary fencing

• Best: one full growing season (spring through fall)

Fence height and placement (important)

• Build the fence from the earth bottom up to 18 inches above the water line.

  • Turtles can climb.

  • Deer and other animals can still jump from shore, so placing the barrier out in the water helps a lot.

Check your lilies often (until they anchor)

• Check regularly at first (especially after storms or animal activity).

• Re-firm any loose soil and re-seat rhizomes.

• Once the plant throws new roots into the soil, your investment is much safer.

Plant “heavy” in natural ponds (this is how you win long-term)

Pond Megastore notes the goal is an established ecosystem where lilies can multiply so wildlife can nibble without wiping them out.
So don’t plant one lonely lily and hope for mercy—plant a colony in natural settings.

Best hardy water lily varieties for natural earth bottom ponds (big + strong bloomers)

These are winter-hardy perennial water lilies currently listed on Pond Megastore, picked for impact + performance in natural ponds.

Big “seen-from-a-distance” showstoppers

• Fragrance and Fortune Hardy Water Lily- Many Huge Yellow Flowers 5-8"

• Wedding Dress Hardy Water Lily- Huge White Wonderful Flowers 5-8"
  
  
• Razzberry Hardy Water Lily- Deep Pink - Easy to see from far away  5-7"
  
  
• Clyde Ikins Hardy Water Lily- Numerous Large Peach Flowers 5-7"
  
  

• Texas Dawn Hardy Water Lily — very large bright yellow blooms (listed 5-7").

• Perry’s Double Yellow Hardy Water Lily — extra-large double blooms (listed 6–7.5").

• Ring of Fire Hardy Water Lily — bold 5–7" blooms and listed as a heavy bloomer.

• Perry’s Orange Sunset Hardy Water Lily — prolific bloomer with a listed 4–6 ft spread.

Heavy bloomers that build strong colonies

• Pin Waree Hardy Water Lily — heavy bloomer that can spread 3–5 ft in the first year (great for establishing).

• Gregg’s Orange Beauty Hardy Water Lily — described as reliable/heavy flowering and suitable for natural earth-bottom ponds.

• Sunfire Hardy Water Lily — medium-to-large spread (3–5 ft) and noted as ideal for natural earth-bottom ponds.

Strong “natural pond” whites and deep reds

• Virginalis White Hardy Water Lily — large white blooms and a listed ~4–5 ft spread at maturity.

• odorata Native American White Hardy Water Lily (species) — classic native look for natural ponds.

• Atropurpurea Hardy Water Lily — dark red blooms that open repeatedly in full sun.

• Cranberry Hardy Water Lily — deep red tones with reliable summer performance when fed.

Fertilizer tabs in earth bottom ponds (yes—you can)

Pond Megastore specifically says that in earth bottom ponds you can fertilize by pushing fertilizer tabs into the soil surrounding the plant.
And if you want “daily bloom mode,” Pond Megastore also emphasizes fertilizer is vital for constant flowers.

Key takeaways (the stuff that saves the sale)

• Plant hardy water lilies on an embankment 1–3 feet deep where there is earth, not all rocks.

• Do not plant in open ponds with carp—carp destroy rooted aquatic plants.

• Wildlife is real: turtles, deer, and nutria can wipe out new lilies fast.

• Use temporary fencing at least 3 months (best = one full growing season), from the bottom to 18 inches above water.

• Check plants often until roots anchor, and plant colonies, not single “hopeful” lilies.