I have a old well in my basement and I want to fill it in so that I can use my basement as a rec room as I want to make this a livable place. I have read about filling it in with clean material, that I understand, but how would I completely make sure it will not flood in the future.

How far below the floor surface is the water? That's the water table. If it hasn't flooded yet, probably won't. Water can't rise in 1 spot and not another. I have never seen water flood from a filled well. This is probably a dug well, considering the age. Start collecting old block, bricks, pavement pieces and dump them in. Then get some broken bags of redi mix, $1 at local HD, and start pouring them into the hole. When you are 6" from the top, make a lattice of rebar to sit on top and fill with concrete. Local codes may dictate particular methods of fill but this is an old country method.