This poem is about the importance of context, essentially. The narrator, possibly Emerson himself, first states that most people and beings in nature don't think of how other people are perceiving them; the "heifer" in the field doesn't think about who might be listening to it lowing, and the country sexton cares nothing for what Napoleon is doing. However, the speaker suggests that such an attitude is the wrong one—"nothing is fair or good alone."
To illustrate this point, he recounts several corroborating incidents. In the first, the speaker hears a sparrow singing, and thinking his song to be beautiful as if "from heaven," he brings the sparrow and its nest home. However, once he gets the sparrow there, it isn't such a great song, because he wasn't able to bring the beautiful context in which he first heard the sparrow (namely the river and sky).
Next, the narrator recalls finding some beautiful seashells on the shore, but once again, when he brings these home, he finds that they have "left their beauty on the shore." Once removed from their context, he finds that they no longer hold the same charm.
Finally, he describes a pair of lovers. The lady, while still a virgin, seems like a "fairy" to her beloved—until she comes to him as a wife, and he realizes that she is not a supernatural creature but a real person.
Knowing these things, then, the speaker determines that he no longer wants to pursue beauty on its own. Instead, he wants to seek truth. As such, he realizes it isn't possible to pick up beautiful things and remove them from their contexts, as they will then no longer really be beautiful or tell their truth. Instead, he determines to commit himself to enjoying things as they are in the moment, absorbing "the perfect whole."