The color shows the amount of dissolved oxygen predicted by the model to be in the water. We model the oxygen at all depths, but the movie is focused on the bottom water, which is where oxygen is often the lowest. When oxygen drops below 2 mg/L (the red part of the colors) that is called "hypoxia" and organisms like crabs begin to be negatively affected. In our region hypoxia typically develops every summer on the continental shelf. In part this is because the water upwelled onto the shelf is already low in oxygen, and in part it is because of phytoplankton blooms near the surface. When these blooms die the organic particles sink to the bottom and when these degrade they use up oxygen.
The movie has a panel at the bottom that shows time. The tide is evident in the twice-a-day variation of the sea surface height. Daytimes are shown as the thick yellow lines on the horizontal axis. Winds are shown by an arrow in the middle of the map, with the scale given by the circle. The light blue lines off the coast on the map are the 100- and 200 m depth contours, the deeper of which marks the "shelf break" separating the coastal region from the deeper ocean beyond.