We conducted acoustical surveys with a horizontal beam transducer to detect fish and with a vertical beam transducer to detect depth and macrophytes in two typical shallow lakes along the middle and lower reaches of the Changjiang (Yangtze) River in November 2013. Both lakes are subject to active fish management with annual stocking and removal of large fish. The purpose of the study was to compare hydroacoustic horizontal beam estimates with fish landings. The preliminary results show that the fish distribution patterns differed in the two lakes and were affected by water depth and macrophyte coverage. The hydroacoustically estimated fish biomass matched the commercial catch very well in Niushan Lake, but it was two times higher in Kuilei Lake. However, acoustic estimates included all fish, whereas the catch included only fish >45 cm (smaller ones were released). We were unable to determine the proper regression between acoustic target strength and fish length for the dominant fish species in the two lakes.