LRunkle,
You ask some very good questions.
The sechi disk only tells you the amount of light absorbed or scattered across a water column. That is all. It is essentially a rough semi-quantitative method to determine the level of TSS. A turbidimeter would give a more accurate direct measurement, but still only tells you quantitative, not qualitative data. Neither differentiate between mineral solids, organic solids (TVSS), and do not discount color bodies such as organic stains from planktonic algae and zooplankton. In the end, you are trying to establish a base of the food chain consisting of a mix of plankton. The sediment doesn't do you any good, and may be doing harm if too high, but usually makes up some of the sechi disk reading. Color also adds to the reading, but does not directly help your needs, other than to provide some additional organic matter that acts to feed the plankton.
If you want a more scientific and direct measurement of the plankton levels, you will need to use a test that is specific for that. That would possibly include a TSS/TVSS anaylsis to back out the amount of mineral solids. You might then need to use microscopic analysis to get an idea of the levels and types of zooplankton and phytoplankton. All of this seems too academic and cumbersome for what you really need. One way to get some idea of what makes up the TSS is to take a sample, add bleach or peroxide to reduce the impact of organics on the clarity of the water, and the residual will be the mineral clays suspended in the water. In my experience, when adding peroxide, if the color changes from tan/green to just turbid opaque, you had the plankton you want.
Probably the best way to meet your needs is to do what Erik says and just use visual observation of color and the sechi disk along with experience to tell you where you are. Use the peroxide test to start to get an idea of what the sechi is telling you, then use that device as an easy way to get data on the fly. As always, the more data you collect, the better the determination you get from the analytics
