El Niño Is Reshaping Aquafeed: What Happens When the Ocean Changes the Feed Formula?

For much of the aquaculture industry, fishmeal and fish oil have been foundational ingredients for a simple reason: they work.

They provide highly digestible protein, essential amino acids and, in the case of fish oil, important long-chain omega-3 fatty acids. They also contribute characteristics that go beyond basic nutrition, influencing palatability, growth, health and the overall performance of a diet. But these ingredients depend on a productive ocean andright now, the ocean is sending a warning.

El Niño is a naturally occurring climate pattern, but its consequences for fisheries can be substantial. Under normal conditions, the waters off Peru and Chile are among the world's most productive marine ecosystems. Strong coastal upwelling brings cold, nutrient-rich water toward the surface, supporting phytoplankton, zooplankton and the small pelagic fish that form the basis of an enormous marine food web. During El Niño, that system changes. Warm surface water moves into the eastern Pacific and the nutrient-rich upwelling system is disrupted. With fewer nutrients reaching the surface, primary productivity can decline, affecting the food available to anchoveta and other small pelagic fish. For aquaculture, that oceanographic change eventually becomes a feed-supply problem.

Peru normally accounts for approximately 20% of global fishmeal production, making changes in its anchovy fishery particularly important to the global market. In 2026, the first North-Central anchovy quota was set at 1.91 million tonnes, but fishing was repeatedly interrupted and only around 25% of the quota had been caught before the season was suspended in June. The result is already visible in global production.

In May 2026, super-prime fishmeal from Peru reached approximately US$2,500 per tonne, compared with around US$1,400 a year earlier. Feed-grade fish oil reached approximately US$4,100 per tonne, up 64% year over year.

Feed is one of the largest operating costs in many aquaculture production systems. When the cost of a key ingredient rises dramatically, producers ultimately face a difficult choice: absorb the increase, pass it through the value chain, or reformulate. Reformulation, in particular, is about much more than replacing protein.None of those options is painless.

Fishmeal is not simply a bag of protein. It contributes amino acids, minerals, peptides and other compounds, while also influencing palatability and feed intake. Replacing it therefore requires an understanding of what the ingredient is doing within the entire formulation. A growing portfolio of alternatives, including plant and insect proteins, algae, single-cell proteins, rendered animal by-products and ingredients recovered from seafood processing, is already entering the market or being advanced through research to help meet this challenge.

Marine Bézagu, PhD, Head of Product Development Aquaculture at Innovafeed, and her team are working with the industry to develop a protein source that offers functional benefits as well as nutritional value, an approach that could prove especially useful during disruptions like the one unfolding now.

"Black soldier fly larvae meal - such as our Hilucia™ Protein for Aqua - isn't just an alternative protein source. By nature, it's a functional ingredient. Growing in a highly competitive microbial substrate, the larvae develop bioactive compounds (antimicrobial peptides, nucleotides, lauric acid) that our processing preserves in the final product. As El Niño strains traditional marine ingredients, the industry's challenge isn't only closing a protein gap, it's maintaining the functional performance fishmeal has always provided, while feed formulations evolve. Our own trials show that BSF larvae meal can deliver both nutrition and function, supporting fish growth and health beyond simple protein supply,"  Bézagu commented on the company’s current product innovation.

El Niño will eventually weaken. Marine ingredient production will recover. But the current disruption highlights a longer-term challenge for aquaculture: building feed systems that are both nutritionally effective and resilient to volatility in global commodity markets. That may mean using a broader portfolio of ingredients. It may mean formulating around functional properties rather than individual raw materials. And it may mean using research to identify combinations of ingredients that can maintain growth, feed efficiency and fish health while reducing dependence on any single source.

El Niño is a reminder that the feed supply chain begins much farther upstream than the feed mill, with ocean conditions, fisheries, ecosystems and climate patterns. That makes feed innovation more than a sustainability conversation. It is quickly becoming a business resilience strategy.