I googled this a bit for you and I think I may found an asnwer: "Right click a dirt block with a crook while a water source is on top to get lily pads (albeit at a rare chance (~1/crook))" This is coming back a few times while looking around, perhaps give it a try?
I tried this and it dosent seem to be working i think it might be an AG2 thing with the clicking on dirt with a crook whilst water is above it
Turns out it needed a view of the sky. Question answered (can someone close this thread idk how to do it XD)