How can I get across water?

At the start of the game, you won't really need to get across any of the
water squares.  The earlier levels are all designed to keep you on dry land,
more or less.

Level 1 doesn't require you to enter either flooded cities or water squares,
and Level 2 only requires that you be able to enter flooded cities.  You
should be able to find the appropriate treading water superpower when the
time comes.

The mission computer will also suggest appropriate routes for travel once you
finally need to cross bodies of water.

But look for blue-ish isotopes and/or an inflatable dinghy, so you don't have
to depend on anything else for travel.