Shakespeare shows the passage of time by referring to "count[ing] the clock" (line 1) and addressing the "brave day sunk in hideous night" (line 2). Thus, he lets us know that time is passing, and day turns to night as the time goes by. The "violet [is] past [its] prime," meaning that its bloom has begun to fade as its season ends (line 3), and black hair becomes "all silvered o'er with white," referring to dark hair that turns gray with age (line 4). The trees become "barren of leaves," further indicating the passage of the season (line 5), and "summer's green [is] all girded up in sheaves" when the harvest is finally brought in during the fall season (line 7).
Old people with "white and bristly beard[s]" also pass away and are laid out on their funeral biers (line 8). The sonnet, then, takes a turn when the speaker wonders if the beauty of his own beloved will go the way of the day, the violet, the sable curls, the leaves, and the harvest, asking if this beauty, too, will go "among the wastes of time" (line 10). He wonders if his lover's beauty will also waste away as a result of the passage of time, just as all of these other things do. These references help to indicate the passing of time in the poem.
A key theme in Shakespeare's sonnets is the passing of time and its inevitable impact on the beauty of the person addressed in these poems. The speaker seems concerned and deeply saddened by the many different reminders of the inexorable nature of the passing of time, which leads him to consider how the beauty of his beloved will likewise fade and diminish, just as in this poem he beholds "the violet past prime" and the "sable curls all silver'd o'er with white." The changing of the seasons as we move from summer into fall indicates the symbolic "death" of the beauty of nature. You might want to consider the images of death that we are presented with: the trees that are "barren of leaves" and the "brave day sunk in hideous night." References to time emphasise the way that all things die and pass into blackness, which of course makes the speaker realise that his beloved to "among the wastes of time must go." The only defence mankind has in the face of death is to procreate, and therefore create images of ourselves that can stand against time a little longer:
And nothing 'gainst Time's scythe can make defence
Save breed, to brave him when he takes thee hence.