The poem celebrates the wonder of nature, symbolized in this poem by a snake.
The speaker is in awe when he notices a snake drinking at a water trough from which the speaker wishes to replenish his water. He has a pitcher with him but cannot proceed with the snake there. The speaker explains, at length, the actions of the snake as it is drinking, as if he is witnessing something so special that it deserves further explanation.
The speaker's admiration for this beautiful creature is obvious, and he feels honored that such a magnificent specimen of nature has made itself visible to him. He is, however, urged by an inner voice to kill the animal since it is dangerous, and he has been taught that such creatures have to be killed.
The speaker, however, resists the temptation because, as he confesses, he liked it too much and was glad that it had visited him and departed peacefully once it had its fill. Furthermore, the speaker makes it evident that approaching a snake and killing it is deemed a manly task. Still, he resists even that contention and refuses to harm the animal.
The speaker questions his courage and motives for not killing the snake. The questions have a rhetorical ring to them and remain unanswered.
It is only when the snake departs that the speaker surrenders to the urge to destroy it and launches a log at the trough. He is fascinated by the snake's hasty departure and disgusted by his own action. He is full of derision and intensely criticizes the fact that he made such a foolish choice. It is apparent that he feels that such a glorious creation did not deserve such ignoble treatment.
The speaker refers to an albatross, which symbolizes a psychological burden. It is as if he resents the duty which has been inculcated into him to be destructive. This, he feels, is his albatross. He wishes that the snake would return.
The reason for the speaker expressing this sentiment is that, in the end, he realizes the snake is a regal creature -- "a king in exile" -- which has now returned to its underground kingdom and he has lost the opportunity to keep company with one of life's greatest creations.
The speaker feels he has to atone for his indiscretion -- his act was a foolish triviality in the greater scheme of things.