It is generally agreed that Holt's disappearance was a simple case of an accidental drowning, but a number of conspiracy theories surfaced, most famously the suggestion that he was a spy for China and had been collected by a Chinese submarine.

[1] As with Menzies, Holt refused a security detail upon taking office, considering it unnecessary and potentially alienating to the general public.

His stance changed after two incidents in mid-1966 – a window in his office was shattered by a sniper, and then an assassination attempt was made on Arthur Calwell, the Leader of the Opposition.

Holt wore a wetsuit so he could fish year round, and preferred either skin diving or snorkeling as he found air tanks burdensome and inauthentic.

He spent twenty-five minutes chasing a large coral trout, but eventually had to abandon the pursuit due to extreme shortness of breath.

[9] In September 1967, Holt began treatment for a painful shoulder injury that he had originally suffered playing football in his youth; he was prescribed painkillers and twice-weekly physiotherapy.

A few days before his death, he had been briefly examined by his personal physician, Marcus Faunce, who advised him to avoid over-exerting himself and to cut back on swimming and tennis.

[8] The Prime Minister is Missing, a 2008 docudrama, suggested that Holt's judgement on the weekend of his death had been impaired by his medication, in combination with work-related tiredness and stress.

On returning home, Holt made plans for the rest of the day, which included a visit to Point Nepean, a barbecue lunch, and an afternoon spearfishing trip.

At 11:15 am, he and four others set out for Point Nepean, where they hoped to watch solo circumnavigator Alec Rose pass through The Rip into Port Phillip Bay.

[16] On the drive back to Portsea, Holt suggested that the group stop at Cheviot Beach for a swim – it was about 12:15 pm, and he wanted to cool down and work up an appetite before lunch.

The school was virtually deserted, as most personnel were on annual leave, but the Victoria Police were contacted and initiated what became "one of the largest search operations in Australian history".

The search for Holt's body was officially called off on 5 January 1968, although it had been gradually scaled back to the point where it consisted only of a daily beach patrol.

[23] Lieutenant-Commander Phil Hawke, who led the HMAS Lonsdale diving team, later stated, "any chance of finding the prime minister was lost by the Sunday night".

[21] Rumours of Holt's disappearance reached the media just over an hour after it occurred,[17] and the first conclusive report was made at about 1:45 pm on Melbourne radio station 3DB.

The service was attended by Fiji, India, Indonesia, Japan, Laos, Malaysia, and Western Samoa sent their foreign ministers as representatives, while numerous other countries sent their ambassadors.

[25] John McEwen, the leader of the Country Party and de facto deputy prime minister, was at his farm in Stanhope, Victoria, when he was informed of Holt's disappearance.

[26] Casey had already conferred with Chief Justice Garfield Barwick and Attorney-General Nigel Bowen, and agreed with McEwen that he should be commissioned to form a caretaker government while the Liberal Party elected a new leader.

[32] Sir Robert Southey, a senior figure in the Liberal Party's organisational wing, said of the events in a 1994 interview: My own feeling about what happened is something like this: [Holt] was a very good swimmer, a very good snorkeler and he came back to Melbourne and troubled, not very well, overstretched, overstrained, worried I believe at the ascendancy which Whitlam was beginning to gain and thinking, "Well now I can relax there's one area in which I really am unchallenged boss, and that's the sea."

In August 2003, State Coroner Graeme Johnstone announced that his office had compiled a list of 103 cold cases involving suspected drownings where bodies were never recovered.

[39] Johnstone also criticised the decision not to hold a governmental inquiry at the time of the disappearance, suggesting that it "may have avoided the development of some of the unsubstantiated rumours and unusual theories".

[13] Who Killed Harold Holt?, a Nine Network television documentary that aired in 2007, gave particular credence to the suicide theory, as did an article in The Bulletin published the same year.

In response, Holt's son Sam gave an interview in which he said "there's no mystery, in essence there's no credibility at all; no one in our family believes it"; Zara had earlier said that her husband was "too selfish" to commit suicide.

[41] Two of Holt's former colleagues, Eggleton and Malcolm Fraser, were also interviewed around the same time, and both rejected any suggestion of suicide; Alick Downer and James Killen had expressed similar sentiments in their memoirs.

A 1968 story in the Sunday Observer claimed that Holt had been assassinated by the US Central Intelligence Agency, supposedly because he intended to pull Australian troops out of Vietnam.

Sol Encel believed that his disappearance marked the end of an interregnum between the stability of Menzies and the internal conflict the Liberal Party experienced under Gorton and McMahon.

[48] Peter Bowers said that Holt's death ended Australia's "age of innocence", as it meant national leaders could no longer keep their private lives completely away from public scrutiny.

[60] Holt's death spawned a storyline in the Australian soap opera Neighbours, and has also been credited with inspiring The Fall and Rise of Reginald Perrin, a British television series.

[61] In 1988, rugby league commentator Jack Gibson – ex-coach of the Cronulla-Sutherland Sharks – said, "waiting for Cronulla to win a Grand Final is like leaving a porch light on for Harold Holt".

Over the following thirty years, opposition fans taunted Cronulla by waving posters of Holt's face and dressing up in wetsuits; the club eventually won its first premiership in 2016.