In chapter 23, Winnie hides the bottle of spring water in a bureau drawer.
Later, in chapter 25, she empties the bottle over her toad. This toad is presumably the same one Winnie meets at the beginning of the story. He is, of course, her special friend, one she unburdens herself to when she is anxious or lonely.
Because Winnie pours the magical spring water over the toad, it is assumed that the animal will now enjoy everlasting life. In the epilogue, we see a cheeky confirmation of the toad's new immortality after Tuck moves the toad away from the road and says, "Burn fool thing must think it's going to live forever."
So, why did Winnie pour the bottle of water over the toad? The answer is that this is the only way to keep the toad cool. In chapter 22, Winnie remarks that her toad seems to be thirsty. She asks her grandmother if she can give him a drink. Her grandmother replies that toads don't drink water; rather, they absorb water through their skin. Before Winnie can catch up to her toad, however, it hops away.
When she next sees her toad in chapter 25, she pours the magical water over him, in order to keep him cool. She also saves him from a dog. Her last words to her toad are telling: "There!" she said. "You're safe. Forever."
Winnie is presumably convinced that her toad will now live forever. For herself, she puts off the act of drinking the water. She decides that, if and when she is ready to drink the water, there will be plenty in the woods.