The entire point of the project is to be able to pump water up the new tunnel when water levels are low...This is what will maintain a pleasant flow level in Waller Creek (which we clearly don't have now and is one of the reasons it is so unappealing down there now). When heavy rains occur, the pumps will be turned off and the tunnel will be solely used to move water to the Lake and get it away from that area of downtown.
As for where the inlet structure is, it is the building that is located on the south (left side on the map JAM provided) side of Waterloo park. It will be part of the retention pond that will be created at Waterloo (there will be a dam to create this pond). It will house pumps to keep the water flowing, as well as debris removal apparatus. From what I recall at one of the meetings, a group of engineers told us that there will be a large grate system that prevents debris from getting into the tunnel, as well as a crane and claw like system that helps scoop the debris into trucks to be taken away (that is why the building back directly onto 12th). The crane is supposed to be powerful enough to handle any large (they said Volkswagen size) debris that would be swept down the creek. There are also a couple of other much smaller inlets along the route to help route water during storms. The main outlet is along the lake, and will allow water to flow into the lake, and also back into the tunnel during calm weather so it can be pumped up to street level and flow pleasantly down the creek. That actually is the main difference between San Antonio's system and this planned one. San Antonio has very little elevation change, making it easy for boats to navigate. This system is closer to a hill country stream than the riverwalk because the water has to flow down about 50 ft. from start to finish.
I don't know if I cleared up any of the confusion (sorry if I made it worse). But if you need more info, the tunnel project website (not the Master plan) should be able to help.
http://www.ci.austin.tx.us/wallercre...htm#tunnel_vid