Some reasons why your pumps aren't pumping:
The pump is more than 2 tiles from water.
The water is salt water.
The best way to build pumps are on jettys of the lowest elevation above water. This way, all of the pumps will be right next to water, and you can pack a lot of pumps in to a small shoreline. This can save a lot of high value residential space near the water. If more pumps are needed, just exend the jettys outward (this trick was used in SC2000 as well, but raising terrain is now cheaper in SC3000).
If the pumps still don't pump, then you've got them beside salt water. Desalination plants must be built in place of pumps. But until 1960, when they become available, you just have to find fresh water, even if it is a long way away (unless you cheat "salf off").
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