When a cotton gin is running, it smells like hay, twigs and “freshly washed sheets,” said Wally Leimgruber, a former cotton farmer. But as is often the case, the gin at the Planters Ginning Company here was silent as Mr. Leimgruber walked the dusty floor one recent afternoon.

Pest infestations in recent decades caused a decline in cotton acreage, and the decline accelerated as fuel costs soared and urban centers like San Diego, about 90 miles to the west, pushed for a larger share of the state’s stretched water supply. Cotton is a water intensive crop, and the fields here are irrigated by canals that draw from the Colorado River, the source of drinking water for much of Southern California.

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