You see flagellates at the early stages of wastewater treatment or when there is log phase growth of bacteria. In lagoon systems, you will often find flagellates predominating near the inlet where dissolved oxygen is low & soluble BOD high. If seen near the effluent, this indicates some type of upset condition. Common triggers include - (1) high hydraulic loads, (2) increased organic loadings, (3) pond turnover, and (4) problems with dissolved oxygen concentrations.
In activated sludge or fixed film systems, the sudden appearance of flagellates can indicate an increase in organic loadings or follow a toxic event that killed off significant portion of the living bacteria found in the MLVSS or biofilm. Either event merits further investigation into what is causing the increase in flagellate populations.