Ag Commissioner Les Wright said market prices dipped last year.
"This was the third year; consecutive year that the west side had zero allotment of water and of course last year the east side didn't get any water either."
Growers enjoyed a wet winter, but the 2016 report still reflects the last year of the water shortage on valley farms.
Farm Bureau CEO Ryan Jacobsen said, "We probably are still going to see some lingering effects in the 2017 crop report, simply because that water allocation came out so late that some of the planting decisions couldn't be made so we may see some ramifications next year."
Fresno now ranks behind Tulare and Kern Counties among the country's top Ag producers. Crop production in Fresno County dipped for the second straight year.
"We hope that this is the low and we start building back up from here," said Wright.
In 2015 pistachio growers took a big hit, many trees produced blanks due to a warm winter but the crop rebounded last year.
"The big change-- pistachios jumped to number seven. It was out of the top 10 crops the year before that," said Jacobsen.
Jacobsen added both wine and raisin grape prices were down last year. Growers continue to pull out vineyards, opting for more profitable crops.
Fresno County's top five crops are almonds, grapes, poultry, cattle, and tomatoes. Mandarin oranges dropped out of the top 10.