It is of course the green light that indicates the location of Daisy, Gatsby's "prize" that he is willing to sacrifice everything for, that Gatsby is so transfixed by at the end of Chapter One when Nick Carraway sees him for the first time. Although at this stage we are not told the significance of the green light, it is clear from what Gatsby is doing and how Nick views this scene that it is of great importance. Consider the following quote:
But I didn't call to him, for he gave a sudden intimation that he was content to be alone--he stretched out his arms toward the dark water in a curious way, and, far as I was from him, I could have sworn he was trembling.
Note how he is almost stretching towards Daisy across the water, expressing his yearning for her and trying to grasp her. The fact that he was "trembling" so violently that Nick could discern it from his location speaks greatly of the kind of emotional suffering that Gatsby is enduring as he contemplates his "grail" that he has sought for so long.