| Summary: | Lake Abaya and Lake Chamo are the two largest Ethiopian Rift Valley lakes; they are located close to each other, but have a strikingly different water transparency. We explain key differences in the structure and the functioning of the food web with variation in limnological variables and major pelagic food web compartments within and across both lakes. Data from a detailed comparative investigation of physical and chemical variables and zooplankton community characteristics during the wet and dry season from two consecutive years revealed major differences in key limnological variables between Lake Abaya and Lake Chamo. The most pronounced differences were related to water transparency and the amount of suspended solids in the water column. Lake Abaya is much more turbid, has lower phyto- and zooplankton biomass, and has considerably lower primary production than Lake Chamo. Based on our results, we infer that the profound differences in food web structure between both lakes probably result from differences in sediment load. Finally, our results indicate that conservation programs should focus on reducing sediment inflow from the catchments into the lakes.
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