1. A method for managing aquifer operation, the method comprising: receiving at an analysis computing device, one or more water measurements from a plurality of sites in an aquifer, wherein water measurements are received at a plurality of time points, and wherein a site includes one or more groundwater extraction wells; calculating well operational data for at least one groundwater extraction well based on the water measurements, wherein the well operational data includes a well efficiency over a time period; receiving an aquifer objective input via a graphical user interface presented on the analysis computing device; generating a pump operation signal based on the well operational data and the aquifer objective input.