>>I wouldn’t think foreign algae would be too much of a
>>problem; they would just get swept up and processed
>>along with all the other trough algae.
Especially if the system were a large recirculating closed loop. Fresh spores of the “good” algae could be introduced just after the extraction point.
The water would recirculate. The algae wouldn't, but the algae spawning plant at the top of the hill would generate more. Thinking about it, even with such a system one might still need to cover the troughs with something transparent to control evaporation. Hmm...