In the 19th century the area suffered frequent attacks from the Ngoni people, who fled north to escape the rule of the Zulu king Shaka, in South Africa.

In April 2002, over 1,000 hectares (2,500 acres) of "corn, rice, nuts and cassava" were washed away at Nkhata Bay after heavy rain, causing a worsening of food shortages.

[12] In March 2006, Nkhata Bay received over 300 bags of maize from the Feed the Nation Fund, because the area was suffering from food shortages.

[14] Malawi's former minister of agriculture, Uladi Mussa Monday, stated in May 2008 that due to heavy rain and flooding, crops in Nkhata Bay had washed away; he said this would cause an "acute food shortage".

In June 2008, it was announced that the African Development Bank (ADB) would fund the reconstruction of the road from Nkhata Bay to Mzuzu.

[23] Each summer there is a multi-day yacht race which starts at Cape Maclear in the south, and ends at Nkhata Bay.

[27] Kasambara caused a storm in Parliament in June 2008 when he pledged 10,000 Malawian kwacha to the Malawi national football team, after their 1–0 victory against Egypt, the African champions, in a FIFA World Cup 2010 qualifier.

[29] There are bars, restaurants, two grocery stores, a bus station, tailor shops, a taxi rank and a market in Nkhata Bay.

[36] In February 2005, the Malawian government announced plans to build ecolodges as a way of increasing ecotourism in the Nkhata Bay area.

Political issues in Zimbabwe has revised the overland backpacking route so that many people now go through Zambia or the Mozambique coast.

While the village now has many places to stay the problem has become attracting people who now often travel through other countries or easier accessed beaches in Malawi.

In March 2000, 73-year-old man from Nkhata and a 22-year-old woman married, in what BBC News reported as "Malawi's surprise wedding of the year"[39] In December 2002, a businessman, Mac Bosco Chawinga, was dragged in to Lake Malawi at Nkhata Bay by a crocodile; Chawinga managed to escape by biting the crocodile on the nose.

[40][41][42] On 9 May 2004, the then-Tourism, Parks and Wildlife Minister Wallace Chiume survived when a boat capsized in Nkhata Bay.

[44] In 2006, the Nkhata Bay AIDS Support Organization was created in Malawi and later registered in the state of Wisconsin as a non-profit corporation.

Over six outreach clinics were established in the past two years, leading to a 23% drop in positive HIV testing results.