Many aquatic plants are flowering plants. Getting them to flower, means duplicating their original conditions.
What is a flower? It is a mechanism that allows plants to exchange genetic material. This means pollen from one flower needs to be transferred to another flower. True, water currents could do this, but the flowering plants evolved on dry land, they are recolonising the water environment. The flowering environment is air born. What this means is that flowers, will only appear underwater by accident. This does happen however, Crypts will "flower" underwater, if their meristem detects the light level variation which triggers flower formation.
There are several strategies in detail, but in simple terms, aquatic plants either send flowering stalks to the surface, or rely on only being underwater for part of the year.
Any surface stalk plant that is kept in suitable conditions will do exactly that. Aponogetons are probably the most reliable group to do this, they send flowering spikes to the surface with abandon. Under suitable conditions, Cabomba, Hygrophila and many of the favourite aquatic plants will produce a special "surface" leaf form often a little waterlily like, and flower spikes rise.
Plants like Swords or Crypts wait until the water level drops, they shed their underwater leaves, throw their emergent leaves, and flower like any other plant you'll find in your garden or a hedgerow.
If you want your plants to flower, find out as much about it as you can, and duplicate the conditions is the simplest advice.
If you have some specific species you are intereseted in, speak up!