The capacity of each reservoir is set by the elevation of the dam, which in turn is set by the water rights accorded to MMWD by the State of California (see next question). Once a reservoir is full, any additional water will flow naturally over the dam’s spillway. We don't have the legal or physical ability to hold on to that water.
When Lagunitas, Bon Tempe and Alpine are full, the overflow spills into other district reservoirs downstream. Water from Phoenix, Kent, Nicasio and Soulajule flows into local creeks where it provides many environmental benefits including habitat for endangered coho salmon and other fish and wildlife. Thus even water that goes over the spillways is put to good use.