Emergy methodology questions were raised during a case study where a Sugar factory effluent were treated in a pond system in the Lake Victoria watershed, and evaluated from a performance, cost and resource use perspective. This paper focus on the methodological questions, which were the following: (1) how should the emergy systems diagram be drawn when dealing with a system that is in the recycle loop? Is the wastewater on top in the energy hierarchy (highest transformity) or should the treatment system be located somewhere between the sugar factory on the energy hierarchy top and the dispersed nutrients low down in the energy hierarchy? (2) Rain emergy dominated the local renewable inputs. But how do rain contribute to the wastewater treatment in a pond system, other than as minor dilution? And is evapotranspiration a relevant measure of rain emergy in an aquatic system? (3) Since the case study had a microeconomic focus, is the historical ecosystem work behind lime a relevant item to include from the company's perspective? (4) the wastewater can be considered as a treatment problem, but also as a nutrient and water resource for e.g. irrigation. How does emergy accounting deal with the dualism of a get-rid-of-view and a get-use-of-view? (5) Is the, among some people, controversial maximum empower theory needed for the evaluation of the system, or is the less controversial energy hierarchy theory sufficient for the interpretation? (6) Does the emergy evaluation add any information regarding the sustainability of the pond system?