The US Customs and Border Protection agency says that 416 migrants have died while attempting to cross the border illegally in 2009 so far.
That eclipsed last year's total of 390. The highest number of fatalities came in 2005, when 492 migrants died.
The increase in fatalities "signal[s] an escalating humanitarian crisis that is not going away and requires more effective governmental responses," the ACLU and the CNDH report said.
"Because of deadly practices and policies like Operation Gatekeeper, the death toll continues to rise"
Kevin Keenan, executive director, ACLU of San Diego and Imperial Counties
The human rights groups' report comes on the 15th anniversary of Operation Gatekeeper, a US border enforcement programme.
Under Gatekeeper, which was passed under US President Bill Clinton in 1994, the number of border guards has been increased and walls and fences have been erected in populated areas.
The policy has encouraged migrants attempting to enter the US illegally to try more dangerous routes, the ACLU and CNDH report said.
"The current policies in place on both sides of the US-Mexico border have created a humanitarian crisis that has led to the deaths of more than 5,000 people," Kevin Keenan, executive director of the ACLU of San Diego and Imperial Counties, said.
"Because of deadly practices and policies like Operation Gatekeeper, the death toll continues to rise unabated despite the decrease in unauthorised crossings due to economic factors."
The groups said that the number of people who have died during unauthorized crossings has increased "in spite of government programmes that attempt to reduce the harmful effects of border enforcement policies and strategies."
Enrique Morones, executive director of Border Angels, a volunteer group which provides help to those who run into problems while crossing the border, told Al Jazeera that migrants were taking bigger risks to cross the border due to the route of the wall and fences.
"There is a 3,000-kilometre border between San Diego and Brownsville - the southern border. Just imagine the hottest desert you have been in, being in the middle of nowhere, not knowing if you are going in the right direction, with a smuggler telling you that you will be over the border in three hours," he said.
"Three days later, you are still wandering around ... it is 130 degrees, there are wild animals, you have people that want to attack you on both sides of the border. There is no human way that you can carry enough water [to survive]."
The human rights groups said that at least 5,600 migrants have died while making unauthorised crossings into the US since Gatekeeper began, citing Mexican foreign ministry sources.
Efforts by various organisations to provide medical and humanitarian aid close to the border so that migrants can receive prompt care have faced increased "government opposition and punishment," the report said.