At least 51 people have died in the past few days as further heavy rain battered Sindh Province, and more rain is forecast in Balochistan.
At least a dozen homes have reportedly collapsed or been damaged, most of them in Karachi. Many others have been flooded.
The governments of Sindh and Balochistan have been put on alert for storms and heavy rain.
"Widespread rains are forecast in the coastal areas of Sindh and Balochistan, especially in hilly areas of Balochistan," Lt-Gen (retd) Farooq Ahmed Khan, chairman of Pakistan's National Disaster Management Authority (NDMA), said in Islamabad.
An estimated 2.5 million people were affected by flooding after four days of torrential rain in Balochistan and Sindh provinces at the end of June, leaving over 300 dead and hundreds of thousands homeless.
According to the UN Office for the Coordination of Humanitarian Affairs, over 6,500 villages were affected and 80,000 houses destroyed.
A lake near the town of Dadu, 300km northwest of Karachi, is close to bursting its banks. Further rains could cause it to flood.
"The situation here is already extremely dangerous. It will be catastrophic if there is more rain," said Ghulam Mirani, president of Pakistan's Fisherfolk's Forum, commenting on the situation at Lake Manchar.
The lake is Pakistan's largest shallow-water natural lake, with some 20,000 nearby fishermen dependent on it for a livelihood.
Lt-Gen Khan said recovery work in the affected areas was continuing and urged all international and local organisations to coordinate relief efforts with the NDMA.
However, levels of dissatisfaction among many remain high.
"We were left to our own devices for days. Even now, we face a situation where our livestock have died in large numbers and our land has been destroyed," lamented Rubina Qadir, 35, from a village near Dadu.
She said her house, made of unbaked bricks, was "still too unsafe" to live in, and that she and her three children were forced to "manage" outdoors as best they could.
While government health teams have been visiting affected areas and have carried out vaccination campaigns, there are still reports of increased incidences of water-borne diseases - most notably acute diarrhoea.
|Flood-hit residents of Balochistan and Sindh provinces complain they have not received enough assistance|
"My youngest son, who is six, has severe stomach cramps and diarrhoea. He is refusing to eat and I have brought him to Dadu to find a good doctor here," said Rubina.
Meanwhile, conditions are said to be still grimmer in affected parts of Balochistan, including the towns of Jhal Magsi, Jafarabad and Naseerabad, which lie along the province's eastern border with Sindh.
"People have received only very limited help and assistance and now diseases are spreading. Many people still do not have adequate shelter, and in the hot, humid conditions prevailing in August, this is contributing to their misery and ill-health," warned Farid Ahmed, provincial coordinator for the Human Rights Commission of Pakistan, in the western city of Quetta.
With the monsoon reaching its full force over South Asia, floods in other parts of the country are also forecast, and the River Chenab, running through Punjab Province, was reported to be flooded on 12 August. However, for the present, it is the situation in Sindh and Balochistan that remains particularly bleak.