The most important light-absorbing substance in the oceans is chlorophyll, which phytoplankton use to produce carbon by photosynthesis. Due to this green pigment - chlorophyll - phytoplankton preferentially absorb the red and blue portions of the light spectrum (for photosynthesis) and reflect green light. So, the ocean over regions with high concentrations of phytoplankton will appear as certain shades, from blue-green to green, depending upon the type and density of the phytoplankton population there.
Reference: http://science.nasa.gov/earth-science/oceanography/living-ocean/ocean-color/