When explaining the impact of commercial overfishing (or, for that matter, terrestrial hunting) on the predator-prey relationships in an ecosystem, conservationists will often talk in terms of changes in population of various species and it is often portrayed as a domino-like effect. This may make it easier for the layperson to understand - a singular, straight line chain of events - but scientists know that the reality of it is a lot more complex. They will speak in terms of a cascade effect, a bit like a nuclear chain reaction, where one event impacts several others, each impacting several others, and so on.
Because of that complexity, there is still a lot that we do not know as to what happens to an entire marine ecosystem when key predators are eliminated through overfishing. We have a tendency to look at just population numbers, but a recent paper in Ecology documented evidence of changes in prey foraging behavior and how this can have a pervasive effect across an entire reef system.
Researchers focused on the northern Line Islands in the South Pacific and studied the foraging behavior patterns of numerous species, using one pristine reef as a baseline for comparison to other areas that were impacted in various degrees by a loss of key predators through local fishing.
The predator-prey relationship is much more than "the big fish eats the little fish." Fundamentally, that may be true but there are also factors such as when and where prey forage that enter into the equation. Some animals maintain certain depth ranges or preferred areas around the reef, or they had particular times of day when they would venture out to feed - all offering a certain level of risk and effecting behavior designed to give them the best chance of survival.
The researchers in the Line Islands found that, with the loss of a predator, prey behavior changed over multiple species, and this, in essence, really upsets the applecart of ecological balance. In fact, the article proposed that, while there can certainly be changes in population numbers of various prey species (which can include predators of smaller species - remember, just about everybody is eating somebody else in the ocean), the changes in foraging behavior could be the more important issue with its effects rippling through the entire complex web of relationships that help to make up a healthy marine ecosystem.
We live in a very complex world, but we have a tendency to prefer our answers or solutions to be neat and simple. Unfortunately, nature hasn't successfully evolved over millions of years in a straight "A + B = C" fashion. With each day, scientists are learning more about that complexity and what profound effects we are having on it.
You can order the complete article from Ecology.