Yeah what he said!
Basically the program generates "potholes" at sea level that rivers flow into but not out of.
Compare that to (for example) the great lakes in North America... Lake Superior sits at about 180 m above sea level (surface) and has a maximum depth of about 400 m (~220 m below sea level). This flows into Lake Erie which has a surface at about 175 m but maximum depth of only about 65 m (~ 110 ABOVE sea level ) then a big drop into Lake Ontario at 74 m above sea level, which then winds down the St. Lawrence river until it gets to sea level at the Atlantic Ocean.
To extend this, lakes tend to sit above sea level, To do this in a program requires manually (or at least I haven't found a nice easy way...?) running the water level up to find areas that would "pool" and be contained when rivers run into them.