Occasionally in science, there are clear causal pathways. We know, for example, what wolves hunt and we can calculate how many elk are in the park. While some scientific questions are cut and dry, most are nuanced. In ecology, there are thousands of species in a given habitat, all exerting force on each other. Additionally, outside forces play a role, be they habitat destruction, highway placement, or pollution. So yes: wolves do change rivers. But it is unlikely that they are the only force changing them. Instead, they are part of a complex web of ecological goodness, making the habitat healthier for all.
The more we learn about science, the more complicated things become and the more difficult it is to draw neat conclusions. But would we have it any other way? We can only see so much from one vantage point. When we view the ecology of Yellowstone looking only for the effect of wolves, we get a majestic picture, but it is incomplete. This does not in any way discount the importance of wolves; without them the ecosystem gets sicker. But when we begin and end our analysis with them, we fail to appreciate the larger tale happening