The soil filters the water. Drilling holes as deep as wells will contaminate the ground water aquifers. When a well is drilled a check valve is installed to make sure the water comes out and does not go in.

The idea has merit however. Large ponding basins can be found all over central to southern California. These collect runoff water in artificial ponds for the purpose of recharging the ground water (soaking in). Most of that water is lost to evaporation and there are steps being taken to limit that as well, like floating solar panels to keep the sun off and limit surface area.

When it rains too much in one year, there just isn't enough capture to make up for the several years of not enough rain.