The top 300 feet of the layer cake is where the biggest nitrate problems are found -- the strata most likely to harbor irrigation drainage, runoff from cities and leakage from septic and sewage treatment.

On the Valley floor itself, there are more clues to the nitrate sources in Tulare County. The county has three distinct sections: a citrus belt to the east; row crops, such as alfalfa or corn, in the center; and large dairies to the west and south.

Nitrates could come from fertilizers used on the citrus and the crops. Large dairies also could be a source.

The dairies get a lot of attention from environmental activists. With more than 1 million head, Tulare County has 20% of the dairy cows in California.

Farmers use dairy waste water to grow crops that cattle eat. With animals that void up to 20 times more than a human, the waste quickly adds up.

The state has rules intended to prevent farmers from overloading the soil and crops with the waste.

In addition, Tulare County began regulating the placement of dairies years ahead of most counties in California. Any new dairy in the county must obtain an expensive environmental impact report, and they are not allowed within a half mile of schools, water wells or homes.

But there are only nine state inspectors for 1,400 dairies in the San Joaquin and Sacramento valleys -- more than 30,000 square miles. The inspectors are spread too thin to inspect every dairy each year.

So dairy owners make their own inspections and report to the board annually.

"They're responsible for sampling the water, soil, crops and the wells on their property," said Doug Patteson, a state supervising engineer based in Fresno.

That's not a good idea, says Starmer of Food & Water Watch. The state should be policing dairies, she says.

Starmer this year wrote a report criticizing the Central Valley Regional Water Quality Control Board, saying there are high levels of nitrates around too many dairies, too few state inspectors and almost no penalties for violations.

Other activists say state rules are not enforced well enough. In 2008, they sued the regional water board, hoping to force more monitoring of all dairies. The court rejected the claim, but the activists are appealing the decision.

Activists involved in the case include Asociación de Gente Unida por el Agua, a nonprofit association based in Visalia. They suspect many communities such as Earlimart, Pixley and Poplar have nitrate problems because of the dairy industry.

But experts say dairies are in the wrong place to be harming water quality along the foothills where there are highly publicized problems.

Like rivers, the water beneath the soil moves downhill -- generally southwest through the county, away from the foothills.

"The groundwater around the highest concentration of dairies moves away from those communities along the eastern side of the Valley," said water engineer Dennis Keller, who has worked on these issues for four decades.

So what's the problem along the foothills? According to one theory, fertilizers used decades ago along the county's citrus belt could be inching into water wells in East Orosi, Seville, Tooleville, Tonyville, Lemon Cove, Ivanhoe and many other small towns.

Another theory: Nitrate is a natural element in the soil. It comes from decaying plants. Maybe that is the problem.

Some speculate the problem is a combination of old fertilizers, natural nitrate and septic systems in the area.

These days, farmers do not apply fertilizer as liberally as they did in the past, mostly to reduce costs and boost efficiency. The practice also reduces nitrates in the groundwater.