You will need to use a mix of defining your lakes as sinks (Create sink structures), and then the ArcHydro function Adjust flow in lakes/streams/sinks. (These functions are only available in ArcHydro for ArcGIS 10.1, I have made a function that might help you on the way if you are in 10.0.)
You can also erase (Extract by mask) the lakes from the raster (get Null values there) to accomplish the same thing, but that'll make it a bit harder to include the water flowing through the sinks/lakes in the end (if water volume is important to your analysis).
Workflows, suggested by the ArcHydro team, can be found here.