The autumn removed the clouds from the sky; the muddiness of the earth and the discoloration of the waters, as abstraction draws away the senses from the objects of perception. The water of the lake, by becoming full, stationary and again declined, performed as if the exercise of inspiring, suppressing and expiring the vital air.

In plain words: Autumn cleared the clouds from the sky, dried the mud and made the waters clear again. The poet compares this to how deep focus pulls the mind away from things the senses chase. The lake filling, staying still and then going down is compared to breathing in, holding the breath and breathing out in yoga practice.