His specific example is a river flowing tan from soil erosion; people who haven't been involved in farming don't necessarily know that the farming is the source of the erosion. I think it's also implied that as fewer people are involved in farming, vastly fewer have been exposed to farming methods that don't cause so much erosion.
Lest you think that Berry puts the "good old days" on a pedestal, he does not. He acknowledges the existence of wise and foolish farming practices dating back to when his parents were farming. He argues, however, that mechanization and the externalization of the costs of foolish practices have led to their increasing adoption.
His bibliography is extensive; if you're looking for a good intro to his work, I'd recommend Our Only World.