For the purposes of developing a TMDL, the Chesapeake Bay's tidal waters have been divided into 92 tidal water segments. There are 35 segments controlled by Virginia and another five Maryland owned segments that include Virginia drainage areas. What are shown by the different colors on the map are Virginia lands that drain to each of those tidal segments.
To understand how the segments are determined we need to remember that the Chesapeake Bay is an estuary or an ecosystem where fresh and salt waters meet. The different water segments are determined by their varying degrees of salinity.
So, the upstream segments that are primarily what we would consider fresh water are much larger (For example, all of the Upper and Middle James drain to the "tidal fresh" segment just above Richmond). Once you get closer to the Bay, with the influx of salt water, the salinities change more frequently, which accounts for the smaller segments.