This study combined several features of acoustic and electromagnetic (EM) waves-based devices including sub-bottom profiler (SBP), side-scan sonar (SSS) and ground penetrating radar (GPR), and in situ sediment data to study responses of bottom sediments after carp removal in Lake Wingra. In 2007, i.e., before carp removal, macrophytes only grew to a water depth of 2 m. Meanwhile, GPR data showed no visible sublayer in vegetated regions, while SBP data revealed a loose and fluffy sediment layer in unvegetated regions, easily affected by wave or current motions. The field data showed that suspended sediment concentrations (SSC) were much greater in unvegetated regions than those in vegetated regions during a one-day wind event, and the resuspended sediments could remain suspended in the water column for two days. In 2009, i.e., after more than half (51%) of carp were removed, the fluffy sediment layer recognized by SBP became thinner or even disappeared, and both SBP and SSS results showed that submerged macrophytes started growing in deeper water. In situ sediment data presented that bulk sediment density and critical shear stress became greater, and bottom sediments consolidated and were harder to be resuspended. Secchi depth collected between 2008 and 2010 was greater than that in the previous 10 years, indicated clearer water state. In short, the fluffy sediment layer because of carp activities may be the main source for suspended sediments to deteriorate water quality. Removal of carp is crucial for stabilizing bottom sediment and improving water clarity in this small lake.