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The groundwater is already contaminated, however, the apron slab can still prevent short-circuiting of contamination down the sides of the borehole casing, particularly if there is not already a good sanitary seal, and hence should prevent the water being contaminated further. The apron slab can also add support to whatever is holding the handpump in place.
The apron slab is also useful for preventing erosion of the soil around the pump which can also adversely affect the fixing of the handpump.
One needs to consider the rainy season when in addition to spilt water there is also potentially flow of contaminated surface water around the pump. I suspect that muddy conditions will soon develop as silt begins to block the sand, which will make water collection unpleasant.
10 - 100 e.coli/100ml far from ideal but is not an extremely high level of contamination. Often people are drinking water with much higher levels of e.coli. My personal feeling is that the risks from using it for bathing are minimal (as long as people don't ingest an water when they are washing themselves or children). I also feel that the risk from washing plates is also minimal. If the plates are dried on plate racks that are exposed to sunshine then I would expect the UV component of the sunlight to kill of most of the pathogens, reducing the risk even further.