I've found that shallow parts of lakes can be fished just like the pools of streams, either with dry flies (if the fish are rising particularly), or with nymphs, or streamers either on a floating or sinking line. However, depending on if you're on the shore or in a boat, if you're after bluegill, bass, or muskie, the types of flies and the depths at which you'd want to be fishing them can vary greatly (and probably a whole page could be written about each different method of lake fishing for each species), so more info about the lakes and type of fishing you want to do will help us give a better answer.
As always Frank is right. Thing is, fish in rivers differ greatly from lake fish. As always we do need to know what kind of fish you are after. Now fish like trout often get to feed on other food stuffs that often let them grow bigger. Often some of the bigger rivers can produce the same results. On the other hand, fish like bass often grow better in a lake over a river. There are many other factors that come into play when lake fishing, that is why what type of fish is so important.