First and foremost, hello. Not sure if this is all going to help, but maybe I can point you in the right direction.
If you don't have a turbidity meter, you can try shining some light through it and trying to gauge what is coming through on the other side. Turbidity is caused by colloids. The size of these particles scatters the light, but depending on your ratio and what not... calculating what's actually in the water could be tricky with that type of analysis. Also, this isn't going to include non-colloidal or partially colloidal molecules (like DNA). Remember that these smaller molecules don't exactly follow your basic ideas of thermodynamics (Brownian motion).
I guess this is going to be part of your bacteria and filtering size problem, but I'll let you decide what's important.
When it comes to trying to find out what's in your 'bioreactor', I'd like to remind you that waste water treatment is usually performed in both aerobic and anaerobic steps. This could be to just reduce the biomass or maybe just use up all the good electron donors/acceptors, not quite sure.
For determining exactly what species, strain or strain sub-type might be in your culture, that's going to be a tougher problem. You can try to find more general ideas using solid media to plate and then get more detailed by finding what they do (or more particularly, what they do not) eat, but something becomes lost in translation. I would recommend using a microscope and trying to get a feel for what your particular batch has in it. You're gonna need a hemocytometer, if you want to get your bacterial size right.
I'm not sure how your seeds filter water, but best of luck and I hope this helps.
-SG
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