It's not just overfishing of coral reefs, it's overfishing everywhere. Fish stocks are declining rapidly, in every bountiful part of every ocean. This is very dangerous, because the majority of the world's population relies on fish as its main staple. It's North America, and to a lesser extent Europe and South America who live more on beef and other livestock.
We're directly polluting it with regular, garden-variety trash. The float-on-the-surface kind. It gets very slowly broken down by solar radiation, where it pollutes the water and poisons the fish. They either die off, or at least become unhealthy to eat. See the link below for an enormous example.
Most large rivers are major sources of pollution. The Mississippi, most of the rivers of India and China, the Niger to a lesser extent - all sorts of toxins and various forms of pollutants.
Climate change, to a *much* lesser extent, is affecting plankton and krill levels, the organisms that form the base of the ocean food chain. Additionally, in the future enormous rise in sea level theories, they could directly kill animals by taking away their natural environments. For instance, to return to your coral, if the maximum 250 foot rise in sea level were to actually happen, the coral would die due to lack of sufficient sunlight, and the animals that depend on the coral would die because they need that environment.
I'm going to pick on some particular nations right now, but the Japanese are hunting thousands of whales per year, skirting the treaties that they signed by calling it "scientific research catch." The Chinese are hunting sharks to the edge of extinction. They catch them, cur off their fins, and just toss them back into the ocean, where, obviously, without fins, they die.
The small changes that have already occurred through climate change in the South Atlantic is putting pressure on penguins (not necessarily the classic tuxedo-style penguins, but the other, lesser known, warmer and more northerly species, such as Magellanic and Rockhopper).
Obviously, offshore and deep-sea oil fields leak oil in small and large seeps and spills - all of which damage the environment to one degree or another.
So... I'm not a tree hugger, I'm just a geologist, but if you know where to look, you can see some form of important human impact anywhere you go.