A rather arcane argument this week about responsibility for water in his government might have given Malcolm Turnbull cause for pause.

When Turnbull became prime minister, the Nationals insisted he include with the usual Coalition agreement about the carve-up of ministerial positions an unprecedented side letter containing extra commitments on policy, among them climate change and same-sex marriage. That the Nationals had these put in writing indicated their underlying concerns, from way back, about Turnbull.

Also among the concessions they extracted in the negotiations was that responsibility for water – with the exception of the Environmental Water Holder which manages and monitors water for the benefit of the environment – was to switch from the environment portfolio, where it came under the Liberals, to the agriculture ministry, held by Barnaby Joyce.

Anne Ruston, a South Australian, was appointed assistant minister. Turnbull wanted to be sure the South Australian interests in the lower part of the Murray-Darling Basin were represented in the portfolio.

Last weekend some Nationals got word that when the formal charter letter setting out detailed responsibilities came, Ruston would have the major day-to-day responsibility for water. They went into action.

Ahead of a meeting between Joyce and Turnbull on Wednesday, there was a lead story in The Australian about the issue. Joyce met independent senator John Madigan, who has had his own concerns with water issues. Subsequently most of the (non-Green) crossbenchers told a news conference, among other demands, that Joyce should have full control over water.

Joyce emerged from his meeting with Turnbull satisfied he would run water day-to-day. But Ruston, with her other responsibilities, will still be involved in the area.

It’s not entirely clear whether there was an attempt to undercut Joyce’s remit or whether the Nationals were jumping at shadows. Possibly it was a matter of the fog of a new administration, as details get formalised. But there is no confusion in the message the incident sent – that Joyce is never shy of a fight.

Why this is especially important is that the future of Nationals leader Warren Truss remains unclear.

While Truss has renominated, there is still uncertainty about whether he will contest the election, with continuing suggestions that he would like to retire then, which would mean he’d step down from the leadership early in 2016.

Manoeuvring for the succession is intensifying, by both the pro-Joyce and the anybody-but-Barnaby camps. Some Nationals who are concerned about the prospect of Joyce as leader are critical that there has not been more succession planning under Truss.

The two most obvious alternatives to Joyce would be NSW’s Michael McCormack and Darren Chester from Victoria. Chester did not do his prospects any good when he came out in favour of same-sex marriage recently.

But both are at assistant minister (Turnbull’s favoured term for parliamentary secretary) level – one step up from a backbencher. The jump to deputy prime minister would be a breathtaking one.

In view of this, among the anybody-but-Barnaby camp there has been chatter about Luke Hartsuyker, minister for vocational education and skills and deputy leader of the House. He has been in the outer ministry since the Coalition was elected and is spoken of as a “safe pair of hands”.

Apart from Truss, Joyce is by far the best-known National. Perhaps he is better known than his leader, certainly since the fracas over Johnny Depp’s dogs. He is a strong retail politician. He was leader of the Nationals in the Senate from 2008 to 2013, when he switched houses and states (from Queensland to NSW and the seat of New England), and has been a cabinet minister and the Nationals’ deputy leader since September 2013.

You would think this experience, plus his popularity in the bush, would make Joyce a shoo-in, given the alternatives. But some in the Nationals are wary of his full-on style. His high-profile opposition to the Shenhua mine in his electorate reportedly does not have majority support among his colleagues.

Some Liberals are terrified at the idea Joyce could be deputy prime minister. While he was prime minister, Tony Abbott had Warren and Lyn Truss to stay at Kirribilli in an attempt to prevail on Truss to go to the election.

The challenge ahead of Joyce is measured by the fact that when the deputy leadership came up in 2013, John Cobb – who would hardly be considered a formidable candidate – ran him close.

The succession weighs on the mind of Truss, a cautious man who brings a great deal of steadiness to his dealings with Coalition matters. It is increasingly preoccupying the other Nationals, whether pro- or anti-Joyce, not least because it is not just about Barnaby but also about how the party will present itself to the electorate and to the Liberals, including Turnbull.