自然と人は渡し舟の多いこの町を通ることになるのだ。 is not referring to nature and people. It's a statement about what people do as one might reasonably be able to deduce given the nature of the situation. It's like saying "naturally" in English. 自然と becomes more like an adverb and not a noun with which something is done.
If we simplify it a little bit, we can see this: 人はこの町を通る. If we find the roots of the sentence we can get a better idea of what's going on around it. So let's start from the idea that people are going through the town.
橋がないせいで means that whatever is happening is happening, as you noted, because there is no bridge. With our new knowledge of what 自然と means, can say infer that whatever is going on is happening as a natural consequence of there being no bridge. So, naturally, people are passing through this town because there's no bridge. But why this town?
渡し船の多いこの町: this town which has a lot of ferries. This is how you should parse this part. の is like が, and この is thrown in at a spot that feels weird for English speakers. But it makes sense. There's no bridge, so naturally people pass through this town that has a lot of ferries. We assume that this status as a port for ferry passage contributes to the town's economic prosperity mentioned in the beginning.
So again, here's how to parse the tricky part:
[ スラウド川には橋がないせいで ] [ 自然と ]->[ 人は [[ [ 渡し舟の多い ] この町 ] を通る ] [ ことになる ] [ のだ ]。
There might be better ways to bracket it all off, but I tried to show where we can split it to get a good idea of what is doing what.
