The development of cities and farms changes the relation of ground water to the Great Lakes:

Block diagram illustrating water resources in developed setting (source: U.S. Geological Survey Circular 1139)

First and foremost, pumping from wells causes less water to discharge to the Lakes or even reverses flow.

Schematic sections showing effects of pumping on natural gw flow to surface water: a) natural, predevelopment conditions, b) moderate level of pumping, c) high level of pumping (source: U.S. Geological Survey Circular 1186)

Some of the water diverted from the Lake by wells can be captured by man-made structures and returned to the Lake as discharge from a storm sewer or water-treatment plant. But in this case the timing, location, and quality of the discharge water is changed from the natural ground-water regime.

Pumping is intense around parts of the Great Lakes:

Map of major pumping centers in Great Lakes Basin for 1990s, U.S. side only (source: U.S. Geological Survey Water-Resources Investigations Report 00-4008)

Pumping has caused flow directions to change and ground-water divides to shift:

Schematic sections of generalized regional ground-water flow lines before pumping began around 1864 and after pumping centers established (source: J.T. Krohelski and D.T. Feinstein, U.S. Geological Survey)

Some ground water that once circulated entirely within the Great Lakes basin now flows to wells outside the basin and is ultimately discharged as waste water to rivers that don't return to the Great Lakes but flow elsewhere (for example, to the Mississippi River):

Schematic block diagram of transfer of water out of Great Lakes Basin due to deep pumping (source: D.T. Feinstein, U.S. Geological Survey)