Water, and ponds especially, are hot hang-out spots in this book, particularly favored by Eustacia. She often meets Damon by the pond near her grandfather's home.
But Eustacia also has one of her earliest, face-to-face meetings with Clym by a well. In fact, the reason that Clym is there in the first place is because the Vyes' bucket has fallen into the well and they have no access to drinking water. However, Clym and others point out that the Vyes could make do with the pond water until they got a new bucket for the well.
"That's the only kind of water we have," she continued, tossing a stone into the pool, which lay on the outside of the bank like the white of an eye without a pupil. The stone fell with a flounce, but no Wildeve appeared on the other side [...]. (3.3.45)
In a way, Eustacia is symbolically acting out her love life with water – by turning down the pond water she's in a sense refusing her link to Damon and choosing Clym instead. And Damon is, of course, a very real presence in that scene with Clym. Eustacia throws a rock as a signal, though it seems she's hoping to catch the attention of someone other than Damon now.
Given how closely water is tied to Eustacia and her decisions (to see or not to see Damon, mainly), it makes sense that water would also be the scene of Eustacia's mysterious death. Did Eustacia choose suicide or did she fall into the stormy water by accident? The question is never really answered. The confusion surrounding her watery demise is fitting, though, given how choices in this novel are never clear-cut either.
Water also plays a huge role in the final moments before Eustacia drowns. She wanders in the rain, ruminating over her life and her life choices.
The moon and stars were closed up by cloud and rain to the degree of extinction. It was a night which led the traveler's thoughts instinctively to dwell on nocturnal scenes of disaster in the chronicles of the world. [...] Never was harmony more perfect than that between the chaos of her mind and the chaos of the world without. (5.7.17)
Water, like many of the symbols in this novel, has both positive and negative aspects attached to it. Water is life-giving and healing, but also deadly and dangerous. So it's fitting that such a complex symbol would be attached to a complicated theme like choices, especially to Eustacia's choices.