When the crest of one wave passes through, or is superpositioned upon, the trough of another wave, we say that the waves destructively interfere.
During any wave interference the shape of the medium is determined by the sum of the separate amplitudes of each wave. We often say that when waves interfere, amplitudes add. During destructive interference, since the positive amplitudes from one crest are added to the negative amplitudes from the other trough, this addition can look like a subtraction.
Watch the above video. Notice that in this animation the crest of the red wave destructively interferes with the trough of the blue wave.