Across 100 profiled companies, "in Australia/New Zealand, 38 percent of highlighted companies are likely to be negatively impacted with 62 percent expected to be positively impacted. In North America the negative/positive split is 45/55 and in Asia the mix is 70/30," it said.
It also expects insurance companies will benefit, while those dealing in capital goods would face headwinds.
"In Australia, El Nino conditions are positive for general insurers. Warmer temperatures lead to higher probability of bushfires, which are the least costly type of insurance event (e.g. compared to hail, earthquake)," the note said. "In North America, better growing conditions will result in strong expected yields in 2016 and therefore benefit crop insurers."
Among capital goods players, it tips Deere & Co. as likely "very negatively" hit by El Nino as corn prices will likely fall on higher yields, leaving farmers will less money to spend on equipment.
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Macquarie isn't alone in forecasting a big impact on the market.
Hamish Smith, commodities economist at Capital Economics, raised his forecast for palm oil to end the year around 2,400 ringgit (around $559) from 1,900 ringgit a tonne in a note Wednesday.
"While a rebound in the price of crude oil supported the initial recovery, the price has also been boosted by increasingly dry conditions in the world's two main producers, Indonesia and Malaysia, as El Nino has raised supply concerns," Smith said.
Indonesia has already been particularly hard hit. The country's meteorological bureau is predicting rains won't begin until December, making for an eight-month-long "very dry" season, Malaysian investment bank CIMB said in a note Tuesday.
That means the country's raging forest fires -- largely deliberately set on Kalimantan and Sumatra islands to clear land for palm oil -- likely won't die until close to the end of the year, the bank noted.
The fires have killed 10 people so far and more than 500,000 there have suffered respiratory infections, the country's national disaster agency, Badan Nasional Penanggulangan Bencana (BNPB), said in a release on its website at the weekend.
"Bottom line is the downside risks to crop harvests have increased, in particular for rice and palm oil," CIMB said, noting the El Nino has the potential to wipe 0.9 percentage point off economic growth over two quarters.
Within the market, CIMB expects El Nino will push up palm oil prices and it tips shares of palm oil players Astra Agro Lestari and London Sumatra Indonesia to rise.
--Robert Ferris contributed to this article.