The shooting took place in the Israeli-occupied southern West Bank, which is normally calmer than the north.
The trio were injured after shots were fired from a moving vehicle at the Tekoa Junction, south of Bethlehem, the IDF said.
The wounded man, in his mid-30s, is conscious and in and in serious but stable condition with gunshot wounds, the Magen David Adom (MDA) rescue service said.
The girls, aged 9 and 14, were mildly injured in the incident. All three were taken to Shaare Zedek hospital in Jerusalem, the MDA said.
Israeli troops are searching for the attackers, the army said.
“We’re talking about an area where there hasn’t been a serious terrorist attack for years,” local mayor Shlomo Ne’eman said in a statement obtained by the Jerusalem Post.
“We all wish a speedy recovery to the person wounded, and embrace the security forces who will soon catch the despicable terrorists, and settle the score with them. We will not give in to the terrorists who seek to spill Jewish blood and throw us out of our country.”
Most of the violence in the West Bank has taken place in the region’s north, especially in Jenin and Nablus. Both those cities have seen Israel carry out deadly anti-terror raids and Palestinian militants attacking civilians, sometimes in response to the IDF operations, in recent months.
The Israeli government and IDF say its military actions in the West Bank are designed to root out terrorist and minimize civilian casualties, though the raids have forced hundreds of families to flee their homes and have seen innocents caught in the crossfire.
A massive operation earlier this month in Jenin saw at least 10 people killed and more than 100 others injured.
Prime Minister Benjamin Netanyahu said that the military was fighting terror strongholds “while doing everything, everything to avoid civilian casualties.” Residents who recounted the incident to CNN described it as traumatic and “horrifying.”