California is awash in water after record-breaking rains vanquished years of crippling drought. That sounds like great news for farmers. But Ron McIlroy, whose shop here sells equipment for plowing fields, knows otherwise. “I’ll be lucky if I survive this year,” he said. Illustrating how broken California’s vast water-delivery system is, many farmers in Central Valley, America’s fruit and vegetable basket, will get just 40% of the federal water they are supposed to this year. Why? Endangered fish. The pumps that transport water from wet Northern California to the semiarid south have been drastically slowed to protect threatened migrating smelt,...