Farmers across the UK are scrambling to finish their harvests and ship their surpluses abroad before the Brexit deadline of 31 October, when a no-deal departure would force them to abandon European markets in favour of Africa.

There has been a relatively good harvest of wheat and barley this year after the rollercoaster weather of 2018, when a freezing spring followed by a record-breaking heatwave wrought havoc. “Exports have continued at a strong pace since the first weeks of August,” said David Eudall, the head of arable market specialists at the Agriculture and Horticulture Development Board.

But he estimates that as much as half of the UK’s likely wheat surplus of 2m tonnes, and 0.5m tonnes of barley, could still be awaiting export by the end of October.

A no-deal departure would drastically curtail access to EU markets, with only a limited amount allowed in at a tariff of €16 (£14) a tonne. Farmers would be left seeking markets in north Africa, where British grain would have to be discounted to compete, leaving many out of pocket.

“The Brexit deadline is having a severe impact with short-term pressure to execute exports before the deadline,” said Tom Bradshaw of the National Farmers’ Union. “This is meaning barley and wheat values have come under pressure and export business beyond the end of October seems incredibly difficult to execute. Not only is freight more expensive but purchasers [in north Africa] often demand moisture content below 14% where our UK specification is 15%, and with a catchy harvest [interrupted by weather] this could prove very difficult.”

While the weather in the south of the UK has been generally good for the harvest, Scotland had its second wettest summer on record and the north of England was affected too. George Dunn, of the Tenant Farmers Association, said there had been a marked north-south divide. “Most of our members in the south have reported relatively good conditions and reasonable yields and quality, whereas in the north [they] have struggled with very changeable weather and yields and quality have suffered as a result.”

Oilseed rape, another key crop for many farmers, was badly affected by last year’s record-breaking heatwave. The drought meant the seeds were planted in dry soil last autumn, leaving the seedlings weak and vulnerable to attack from the cabbage stem flea beetle, a pest that used to be controlled with neonicotinoids, banned because of the damage they cause to bees.

Farmers growing other crops also face an uncertain autumn. While soft fruit yields have been good in some areas – blackcurrants enjoyed a bumper year – vegetables have provided mixed results, according to Jack Ward, the chief executive of the British Growers Association.

Cauliflowers have been in short supply because of poor weather in their key growing season in the UK, and the heatwave across Europe. While rainfall in May and June “saved the crop” for wheat, according to Eudall, floods in Lincolnshire in June struck at the heart of some of the UK’s most productive farmland, affecting crops from cauliflowers and cabbages to potatoes and onions. “That was an extraordinary wet spell, and Lincolnshire accounts for a lot of [vegetable] crops,” said Ward.

Consumers are unlikely to face serious shortages of British-grown crops, though retailers have warned of problems with warehousing and imports in the case of a no-deal Brexit. “There are still three months left to Christmas [harvests] in which good and bad things can happen,” Ward added.

Many farmers were thrown into panic by the shock announcement by Priti Patel, the home secretary, that free movement would end on 31 October, which would have left them facing hiring shortages in the key pre-Christmas season. There was a government U-turn, but in the medium term the issue remains a serious worry.

The government’s estimates of the harvest will be published in early October. A spokesperson for the Department for Environment, Food and Rural Affairs said: “We’re committed to championing our farming sector and ensuring we seize the opportunities offered by Brexit. We have already introduced a new seasonal workers pilot to help make sure our farmers have the workforce they need and have guaranteed the same cash total for farm support until the end of the parliament.”