One of the hardest things to get a mental grasp on while contemplating fishing on the larger Fingerlakes (i.e. Seneca and Cayuga) are the fish migrations that take place. These migrations confound a lot of area anglers, as well as many of the tourists that fish the region. Fish need food, spawning habitat and wintering areas. If they can't find what they need, they move (migrate) to find it. There aren't many areas on Seneca and Cayuga Lake that provide all of these things.
Huge lakes like Seneca and Cayuga are actually fairly hostile fish habitats - at least for warm water species. The vast majority of water on Seneca Lake is too deep to support the species we fish for - like smallmouth bass, pike, perch and other panfish. Most of Seneca Lake is well over 100' deep! Not only is the lake incredibly deep, it's also very cold and the water temperatures are very volatile in the springtime. Fish like smallmouth bass need water temperatures that remain fairly stable in order for their eggs to hatch and the fry to succeed.
Cornell did studies on smallmouth bass in the late 1940s and early 1950s. They found via tagging and tracking studies that the bass make huge migrations in Cayuga Lake. Fish will winter near Taughannock Park and around select other south end areas, then many of them will migrate to the northern portions of the lake in order to spawn in the springtime. Then they gradually move south. Lake trout do similar things. Pike move as well. Areas like Cayuga AES load up with pike in the wintertime. Try fishing around AES in May and June and again in the fall and you'd be lucky to catch a pike or two! These fish are moving there from a long ways away! Perch move too. The presence of alewives makes fishing the Fingerlakes even more confusing - since they move around A LOT!
Fisheries Departments haven't really studied these migrations much - so it's mostly local knowledge. I intend to read some studies conducted elsewhere on pike migrations and things of that nature. But for now, know that for many species on the large Finger Lakes the motto can be summed up by saying "Here today, Gone tomorrow!"