Agrium shares were down Thursday, after the company issued lower guidance for the second half of its fiscal year, citing strong growing conditions.
"You just don't need a lot of fertilizer when things are real good," Cramer said on "Squawk on the Street." "If you're a farmer, you're doing great … but you don't need more fertilizer and you may not need more seeds."
In turn, he thinks Agrium's woes could reverberate throughout the ag sector, at least in the near-term.
"People sell first and ask questions later," Cramer said. "I think people are going to say, 'Oh, Agrium. Farm complex. Let's sell Monsanto. Let's sell Syngenta. Let's sell Deere. Let's sell Agco. Let's sell Potash. Let's sell Mosaic.'"
"All of those are going to be weaker. The whole complex," he said.
Eventually, Cramer thinks the seed stocks will be a "buy." The fertilizer stocks may continue to struggle, though, he said.
DISCLOSURE: When this story was published, Cramer's charitable trust did not own AGCO, Agrium, Deere, Monsanto, Mosaic, Potash,or Syngenta.