Of course there is a difference.
1-He used to swim in this river when he was young.
" Used to" describes something that happened regularly in the past but no longer happens today. The speaker in this example no longer swims in that river because it was just a past habit that no longer exists.
2-He often swam in this river when he was young.
The past simple, in contrast, simply situates something in the past. This person might still swim in that river today.