Raphael Were Owaka cuts an incongruous figure in his bright yellow oilskin despite the warm sunshine as he stands above a huge pond, filled with fingerlings – fish the size of a thumb.

The tall 61-year-old has just led a group, squelching through waterlogged fields, to show 18 ponds to harvest tilapia, which have been practically fished out of Lake Victoria, about an hour away. The lake provides more than 90% of Kenya's total fish supply, but dwindling stocks have pushed up the price of fish in western Kenya where almost 60% of households are dependent on fish as a source of income, either directly or indirectly.

The ponds form part of a Kenyan government initiative to push aquaculture – a successful concept in Asia – so it can provide an alternative to small farmers who are scrabbling to eke out a living from the poor soil. But through a cruel irony, the current drought that has devastated the Horn of Africa, with more than 12 million people requiring emergency food aid, threatens to scupper efforts to promote aquaculture, at least in the region around Kisumu, Kenya's third largest city.

"We have never experienced such a dry spell as the past year," said Owaka, who owns three ponds. "The ponds dried up and we had to prematurely harvest the fish before they became big."

The fish harvested were less than 100 grams instead of 250 grams – "dinner plate size" – to fetch the best prices. But with the ponds rapidly drying up, the fish had to be harvested in November otherwise the harvest would have been totally lost.

The hope is that the megapond of 80 square metres, 3 metres deep, will serve not only as a giant fish tank but as a reservoir for the smaller ponds of 30 square metres. The big pond, holding 20,000 fingerlings, took 40 days to dig, and involved four men and 96 women. In Kenya, women seem to do much of the agricultural work, from fetching water to digging terraces and irrigation pits

"In Kenya, women do all the work and the men drink," one young Kenyan joked.

But the drought is no joking matter. The government's aquaculture scheme, announced in 2009, but which got going only last year, depended heavily on a good first successful harvest that would generate enough income for farmers not only for them to buy food and pay for their children's school fees, but to buy the stocks and feed for the next eight-month cycle.

Fish farmers by a pond in Kisumu, Kenya. Photograph: Mark Tran/guardian.co.uk

Now, however, the local authorities are worried that last year's premature harvest may have deterred farmers from pressing ahead with fish farming. The government provided fish stock on a one-time basis, but after that farmers were on their own.

"People have not accepted that they had to restock for themselves," said Susan Otieno, project co-ordinator for Farm-Africa, an NGO taking part in the "aquashop project", a two-year programme backed by £322,000 in funding, that supplies commercial and small-scale fish farmers with the essentials for farming, offers technical advice and training, and link farmers to markets.

Abigael Achayo, 57, a widow with four boys and thee girls aged from 17 to 30, is undeterred. One of the beneficiaries of the government's scheme, she sees fish farming as a better alternative to traditional farming. "I think it is better than crop farming, crops can sometimes fail, this offers more security," she said Achayo, who is still waiting for her batch of fingerlings, even though her pond was dug last October.

Cecil Comte, 21, is even more gung-ho. Although he made less than expected because of the drought, he sees fish farming as preferable to making bricks. Dotted in the wet fields around the fish ponds are piles of bricks. Poor soil still has its uses,

"This time I'm hoping for the maximum, 1,000 fish, plate-size, at 200 shillings," said Comte. "I want more ponds and I want to become rich."

Boosting economic prospects

The area around Kisumu, which has a population of 3 million, suffers from a high poverty rate. About 70% of the population live on less than $1 day, partly because HIV and Aids hit so many families. Small-scale fish farming is seen by the Kenyan government as a way to boost economic prospects, not just in western Kenya, but throughout the country.

Initially, 160 out of the country's 210 constituencies were identified for government-backed ponds. Each was awarded 300 ponds making a total of 48,000, with each pond getting either 1,000 fries (tadpole size) or fingerlings and fish feed. The scheme has run into teething problems. There was only one hatchery of any size, an American company, Dominion, from which to get supplies – and it could not meet the huge government order. Cronysim was another problem, with local bigwigs insisting they get their ponds, even though their land was not suitable. Some soon lost interest as fish farming is far from straightforward; it is a highly technical business.

The right fish feed – pellets that contain soya, sunflower oil, cotton oil and amaranth – is expensive. Feed for an eight-month cycle costs $340, which is a lot for a small farmer already struggling to make ends meet. Apart from the expense, the farmers needed know-how. The aquashop concept was designed to spread the expertise and training that novice fish farmers needed.

Owaka, besides being a pond owner, is one of the six aquashop owners in the region. His shop in Oboch, a tiny market centre at the end of a muddy road barely wide enough for a car, is some distance from the main road. His shop stocks feed, nets and twine, which can be stretched across the ponds to fend off birds such as pelicans, which are one of the main predators. Snakes and thieves make up the other predators. Out of 1,000 fish, a farmer is doing well if they can harvest 800.

Otieno says this month will be crucial in determining how many fish farmers in Kisimu have decided to drop out because of the impact of the drought. Her goal is that those who stick it out will be able to deliver good quality fish to supermarkets, restaurants and hotels in Nairobi, because the demand is there.

As for Owaka, he is an unstoppable advocate of fish farming, with a keen thirst for knowledge. "We were locked in our box of no knowledge," he said. "Now we are out of the box and we can fly to the skies."