A group representing the bereaved families organised tributes, including a silence at 6:29am - the minute the attack began - and a ceremony that will follow tonight in Tel Aviv.
Israelis gathered in a moment of silence on Wednesday to mark three years since the Hamas-led attack of 7 October 2023, which a UN inquiry confirmed killed 1,200 people and saw 252 taken hostage.
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In southern Israel, families mourned at road junctions, bomb shelters and the site of the Nova music festival, all places overrun by militants in the deadliest attack against Israel.
It is the first anniversary on which all the hostages are home, bringing a new phase of mourning.
Among those marking the day was Elkana Bohbot, 37, who was abducted from the Nova festival and is spending the anniversary in Israel for the first time. He was freed last year after 738 days in captivity, most of it in a tunnel 50 metres underground. He said his daughter's birth in August this year was his message to his captors that "we [Israelis] were here, and we will always be here forever".
At the site of the Nova music festival, where Hamas militants in trucks and paragliders opened fire around dawn on October 7, family members bowed their heads in silence, although AFP reported at least one put on techno music in tribute to the fallen.
Both at Nova and the Kfar Aza kibbutz, another site of mass killings three years earlier, AFP reporters heard loud bangs from across the border in Gaza during the commemorations as Israel carried out new strikes, despite a ceasefire officially in place for the past year.
Gaza officials said at least two people were killed in overnight strikes in the territory, most of which has been reduced to rubble in relentless bombing in retaliation for the worst attack ever against Israel.
Wednesday's gatherings were separate from the government's official memorial services, held on 5 October to fall closer to the anniversary in the Hebrew calendar.
He vowed there would be "no forgiveness for the murderers" and promised never to allow Hamas to rule in Gaza.
More than 200 former hostages and relatives wrote to Netanyahu last year demanding an inquiry into the 7 October attacks or his resignation but Israel's leader opted to publish redacted government documents instead of launching an investigation and described the attacks as "a serious intelligence failure".
An election follows at the end of the month.
Up to 75,000 Palestinians have been killed in Israel's retaliatory campaign, according to the UN.
The UN said this summer that about 1.7 million Palestinians, roughly 80% of the population, were living in tents and temporary accommodation while Israeli maps show more than half of the Gaza strip is now controlled by its troops.