West Coast farmers launched an urgent application in the Western Cape High Court on Monday concerning water rights, which may have far-reaching consequences for agriculture.

At the heart of the case is whether it is lawful for irrigation boards to approve the transfer of water rights from one farm to another in a board's area of jurisdiction.

Irrigation boards have been doing this for years with the knowledge of the Department of Water and Sanitation.

The boards function as "water management institutions" in terms of the National Water Act.

Then, in January 2018, the department had a change of heart and sent out a circular saying it was unlawful for irrigation boards to do so.

This caused consternation in the agricultural sector. The fear is that the system may fail if decisions about water rights transfers now have to be decided by a few officials in Pretoria, instead of being dealt with by irrigation boards around the country – each with an intimate knowledge about the farming situation in its area. Without water rights, many farms could not function.

Wittewater Boerdery Pty Ltd and Groot Winterhoek Koelkamers, farming operations near Piketberg, have launched court proceedings against the Minister and the Department of Water and Sanitation regarding the temporary transfer of water rights.

Wittewater Boerdery is asking the court to allow it to transfer 227 hectares of its water use rights to the farm Zanddrift near Malmesbury, pending a decision by the Water Tribunal.

The companies have approached the court on an urgent basis as they say the Water Tribunal is currently dysfunctional because it has no chair and is unlikely to have one appointed until April 2019.

In the meantime, crops have to be irrigated.

The companies have also asked the court to rule that the Minister and Department of Water and Sanitation shall not interfere with the transfer of these rights.

Johann Conradie, farmer and director of the two companies, said members of the irrigation boards had intimate knowledge of farming activities in their areas of jurisdiction, of the availability of water and the effect the temporary water transfers would have on the water scheme. All this was taken into account when it approved such transfers.

The Lower Berg River Irrigation Board has approved the annual temporary transfer of water to the farm Zanddrift for years.

In August 2017, the Department of Water and Sanitation issued a directive that Zanddrift must cease taking water from the Berg River as it was not entitled to do so.

Serdyn Boerdery, which manages Zanddrift, said in court papers that if it were prevented from using the water rights, it would have "devastating consequences", particularly for a wheat crop worth R6-million.

However Rashid Khan, regional head of the Department of Water and Sanitation, denied that the department had acknowledged the right of irrigation boards to transfer water use entitlement.

Khan conceded that the department's 2018 circular had been "hotly debated" since it was issued in January, but said until a court set it aside, it remained department policy. The department, not the irrigation boards, would decide on transfer of water rights.

Khan argued that since the applicants had already put the matter before the Water Tribunal, that process should be completed before they could approach the court.

He denied that the tribunal was dysfunctional and said the deputy chair could deal with the matter.

However, Conradie replied that Khan was being "disingenuous" by saying the Water Tribunal was functional.

It was of concern that Khan and his department were silent on the reason why a practice that had been carried out by irrigation boards for years had suddenly become "an unlawful activity".

"Does the department intend to prosecute all members of irrigation boards who transferred water rights over the last 15 years? If the answer is yes, I predict it will bring extreme harm to the agricultural community," Conradie said.

He argued that the irrigation boards' actions were lawful in terms of the National Water Act.

He said the department’s 2018 circular claiming this was not the case "cannot trump the provisions of the act and cannot legitimise conduct of the department that is in conflict with the act".