1.  Habitat loss -  As our world becomes more developed, we are losing important ocean habitats. It is projected that 25 percent of all species may be extinct by 2050.
2. Overfishing and bycatch - Growth in demand for seafood and advances in fishing technologies have outpaced the ability of the ocean to replenish itself. Most of the world's fisheries have collapsed, or are on the brink of collapse. Another problem is the unintentional captures of non-target fish as well as seabirds, marine mammals, and turtles - called bycatch.
3. Pollution - Over 80 percent of marine pollution comes from land-based activities including factories, farms and urban areas (lawns, streets, parking lots and storm drains). Mineral and energy development off the coast, including offshore drilling, can also have serious impacts e.g. the Gulf of Mexico Oil Spill.
4. Climate change - Rising levels of greenhouse gases, including carbon dioxide, have many ocean impacts including coral bleaching, ocean acidification, melting glaciers and rising sea levels, increased and more intense flooding and storms, and shifting weather and ocean circulation patterns.
5. Invasive species and disease - 95% of foreign trade in US is moved by ships. Ships can bring invasive species, such as zebra mussels and asian carp, in their ballast water and release them in ports and major lakes. Coastal pollution is often the source of infectious disease in both humans and other marine species, and their spread is enhanced by trade and climate change.

Learn more about these issues at:

Aquarium of the Pacific: http://www.aquariumofpacific.org/10/ocean_on_the_edge/ocean_issues/
National Geographic: http://ocean.nationalgeographic.com/ocean/critical-issues/
Smithsonian Ocean Portal: http://ocean.si.edu/ocean-and-you/
The Nature Conservancy - Global Marine Initiative: http://www.nature.org/initiatives/marine/about/