Fall care depends on the kind of aquatic plant you have and how cold your pond gets. Identify which plants are hardy in your climate, clear away decaying growth, and plan ahead for containers that could freeze solid.
Hardy marginal plants
As growth slows and leaves yellow, stop fertilizing hardy marginals for the season. Remove dead foliage so it does not collect in the water. Many can remain in the pond over winter, but follow the plant's own hardiness and planting-depth guidance. Where wildlife habitat matters, you can leave some sound stems standing and tidy them in spring.
Hardy waterlilies
Remove spent leaves and flower stems as the plant enters dormancy. If a container sits in a shallow area that may freeze through, move it to a deeper, nonfreezing part of the pond when appropriate for the variety and local conditions. Don't assume every pond has a safe depth; check the plant label and your winter conditions. For planting basics, see How to Plant a Waterlily in a Pond (and Mistakes to Avoid).
Lotus and tropical plants need a separate plan
Wait for lotus foliage to die back before trimming; avoid cutting green hollow stems. Keep its tuber from freezing according to the variety's care guidance. Tropical marginals may be brought indoors where outdoor conditions are too cold, but light and moisture needs vary by species. Tropical waterlilies can be challenging to overwinter; seek variety-specific storage instructions rather than treating them like hardy lilies. Some gardeners choose to replace tropical plants the next season.
A quick fall check
Remove decaying material, identify containers exposed to freezing, and make a species-specific plan before the first hard freeze. For whole-pond winter preparation, read Tips for Winterizing Your Pond.
A little cleanup and the right cold-weather placement can make spring startup simpler, without assuming every plant needs the same treatment.