No one has been prosecuted for the murder.
Estemirova had been reporting on the torture, disappearances and murders of people in Chechnya, and she knew there was a risk to her life.
Two years earlier, her friend Anna Politkovskaya, a journalist and prominent Kremlin critic, was shot dead in her apartment building in St Petersburg.
In a joint statement published in the Washington Post on Monday, women Nobel Peace Prize laureates and winners of the annual Anna Politkovskaya Award - given to female journalists or human rights activists in conflict zones on behalf of RAW in War - wrote that "no adequate investigation into Natalia's murder has taken place, nor has anyone been brought to justice for her killing".
Amnesty and Human Rights Watch are also among the organisations who have raised the alarm on the anniversary.
They have urged Russia to take action.
Mariana Katzarova, the head of RAW in War, who was close to both Estemirova and Politkovskaya, said Estemirova stood up to the Chechen leader Ramzan Kadyrov during a meeting in Grozny in 2000 in which he threatened to kill Politkovskaya.
"I met them both just a couple of hours after this meeting. I saw Anna crying for the first time. It was a miracle that they left safely this time. All because of how brave Natalia was."
In 2007, Estemirova became the first recipient of the annual Anna Politkovskaya Award for her work in Chechnya.
"It's never been a more dangerous time to be a journalist and human rights activist," said Sarah Clarke, head of Europe and Central Asia at ARTICLE 19, an NGO defending the freedom of speech.
Threats against journalists are at their highest level in a decade, she said.
Dozens of journalists are killed every year around the world in war zones or countries with weak rule of law, where perpetrators are brought to justice in one out of 10 cases.
Female journalists and human rights activists face greater threats.
A 2018 report by the International Women's Media Foundation (IWMF) found that two-thirds of female journalists and media workers have experienced physical, sexual and/or online abuse. Twenty percent of women did not report the incident, more than half of this group said they did not think it was important enough or that anything would be done.
Hostility towards journalists is becoming normalised around the world, amid a global rise of "strongman" populist leaders around the world who routinely demonise journalists, said Clarke.
"With the rise of populism, institutions such as the judiciary, police and investigative bodies, that are supposed to protect journalists have weakened," she added.
US President Donald Trump calls media "the enemy of the people" and Turkish President Recep Tayyip Erdogan has branded some journalists as "traitors".
rhetoric is "extremely dangerous because it paves the way for threats and violence which can ultimately lead to assassinations", said Clarke.
The lack of protection for journalists and activists in conflict zones threatens to keep human rights abuses hidden.
Kholoud Helmi, a Syrian journalist and co-founder of the newspaper Enab Baladi, was forced to flee Syria in 2013. She left her hometown of Daraya, a suburb of the capital Damascus.
"Leaving was not a choice," said the journalist and the 2016 recipient of the Anna Politkovskaya Award.
The previous year, four of the paper's founders were arrested by the Syrian authorities, one of whom was killed under torture in a detention centre.
Helmi helped to create Enab Baladi in 2011 as a platform to expose the atrocities committed by President Bashar al-Assad's government.
"There were no international media organisations in Syria to report on what was happening. The regime persecuted them and the state-owned media only reported the regime's point of view," she said.
Women made up 75 percent of the paper's founders.
"We were able to write about what it's like giving birth in the middle of conflict and what it's like for a mother when her son goes missing," said Helmi.
Women risked their lives to distribute the paper in Syrian cities.
"We were able to pass unrestricted through checkpoints as the guards usually didn't search women," said Helmi.
She was, however, stopped by security forces several times and knew well she was standing between life and death.
"The demand for these stories and the fact that my friends had lost their lives gave me courage," she said.
In 2013, she and other Enab Baladi founders started their journey to Turkey, where they continue to work today. The paper continues to cover news from all over Syria through reporters spread across the country.
In danger from Pakistan to Malta
In Pakistan, where a conflict between the Pakistani military and armed groups has killed thousands of people and uprooted millions in the country's northwestern regions since 2004, journalists and activists are increasingly under attack.
The authors of the joint statement on Natalia Estemirova wrote that they are "gravely concerned" about human rights activist Gulalai Ismai, who was forced into hiding since she was charged under anti-terrorism legislation and banned from leaving the country last June.
Ismai was targeted after speaking out about the government's inaction over therape and murder of 11-year-old Farishta Mohmand in May.
"The war economy has snatched humanity out of this society. There has been a startling increase in sexual abuse and murders of children thanks to the brutalisation of society. War increases the crime of sexual assault," Ismai tweeted in May.
In 2018, Human Rights Watch wrote that counterterrorism laws continue to be "misused as an instrument of political coercion", including against journalists and activists, and "many defendants are denied the right to a fair trial".
Women are not only targeted in conflict zones.
In October 2017, Maltese investigative journalist Daphne Caruana Galizia, 53, was killed in a car bomb attack. No one has been prosecuted in connection with the attack.
Her death was believed to be connected with her work in exposing Malta's links with the Panama Papers document leak, which revealed the identities of wealthy individuals and public officials with offshore holdings.
The Maltese government, a member of the Council of Europe and a party to the European Convention on Human Rights, had "fallen short on all national and international standards in investigating Daphne's death", said Clarke. "None of the politicians that Galizia wrote about were interviewed. That's extraordinary," she added.
Clarke is "extremely concerned" to see that the cycle of abuse against female journalists in Malta is repeating itself.
Caroline Muscat, the founder of the investigative online outlet Shift News who has carried on with some of Caruana Galizia's investigations, has increasingly faced death threats and online harassment.
"It shows us the Maltese government has learnt nothing."
The authors of the joint statement wrote: "The international community appears powerless to prevent the attacks and the killings, and to provide protection and safety to those facing grave danger."
Political will is the most essential way to keep journalists safe, said Clarke.
Without it, women journalists and activists are forced to risk their lives for refusing to let human rights abuses go untold, for writing the truth.