On maps without a river, brook, any underground soil or aboveground plants to gather (so you can therefore get their seeds and begin farming aboveground) these can be a blessing since they provide water for muddying tiles (allowing both farming and plant gathering underground), but on others they can be a hindrance, because you have to dig around them.
The underground river is populated with frogmen, lizardmen, snakemen, olmmen, cave crocodiles, giant toads, giant olms, and mud men. These can interrupt the work of any dwarf within line of sight, and can thus be a real nuisance.
The water sources for an underground river, if they are present on your map, are waterfall tiles "from nowhere". Correspondingly, an underground river will terminate in a waterfall that drops into a chasm at the bottom of the map.
Underground rivers are 2 to 5 tiles wide and while they often flow in a straight line, they can twist and turn across the entire map, spanning multiple levels.