Chief Insp. Julio Go, Isabela police operations chief, identified the drowned victims as Joey Quirabo, 36, of San Pablo town, and Eugenio Alonso Jr., 25, of Benito Soliven town.
He said Daniel Gonsay, 13, remained missing after he was swept away by a strong current while he was crossing the Danipa creek in Echague town.
Isabela PDRRMC reports said at least 24 villages were flooded in the towns of Delfin Albano, Cabagan, Sta. Maria, Palanan and Tumauini.
The following bridges remained impassable on Wednesday: Masaya in San Agustin, Alicaocao in Cauayan City, Sto. Domingo-Santiago in Quirino, Banquero in Reina Mercedes, Colorado and Dipacamu in San Guillermo, Annafunan and Gucab in Echague, and Calinaoan in Sto. Tomas.
Several roads were also flooded in Palanan and Dinapigue towns.
In Ilagan town, floodwaters started to recede in some parts of the capital on Wednesday. At least five houses collapsed, while a 300-meter section of a road in Barangay Cabiseria 5 was damaged due to the floods.
The Ilagan town council declared a state of calamity on Tuesday after at least 50 villages were hit by floods.
In Cagayan, about 22,000 residents in Tuguegarao City and five other towns have been affected by the recent floods caused by the swelling of the Rio Grande de Cagayan, reports from the PDRRMC said.
Worst-hit were Solana and Amulung towns, with 8,260 and 7,016 residents, respectively, who are living in villages on the banks of the river, said Resty Vargas of the Cagayan PDRRMC.
In Tuguegarao City, 254 people had to seek higher ground while others stayed in schools and day-care centers as floodwaters rose to about 5 feet in low-lying communities along the Pinacanauan River.
The flood also submerged the overflow bridge there, along with the Maguilling bridge in Piat and Tawi bridge in Peñablanca, rendering these impassable, the report said.
In Aurora, Mayor Reynaldo Bitong of Casiguran town said floodwaters in the town proper started to recede on Wednesday, down to at least 3 feet from 4 feet on Tuesday.
Mayor Victor Briones of Dilasag town said floodwaters in the town rose to about 3 feet on Wednesday.
Reports from the Office of Civil Defense (OCD) in Central Luzon said the six fishermen who were reported missing in Casiguran town on Tuesday had been found alive.
The OCD said the road connecting Casiguran and Dilasag remained impassable due to the swollen Minanga and Casalucan Rivers.
Some 300 people who fled to evacuation centers in the two Aurora towns have started to return home, said Nigel Lontoc, OCD assistant regional director.