In a statement, Maj. Gen. Chris Olukolade said that "a large number of terrorists ... drowned" in Lake Chad and others were killed in the fighting to take the fishing town.
Lake Chad touches four countries -- Nigeria, Chad, Niger and Cameroon -- all of which have been targeted in recent weeks by Boko Haram, the Islamist extremist group blamed for ongoing horrific attacks, abductions and other abuses.
According to Olukolade, Nigerian troops entered Baga early Saturday morning and, hours later, moved into a "comprehensive ... search phase (to) mop up arms and ammunition and also apprehend any terrorist who might be hiding in the vicinity."
The operation in Baga was one of about a dozen being carried out in the region, all part of a Nigerian offensive aimed at ultimately crushing the terrorist group.
"The troops are now dominating and conducting aggressive patrols...," Olukolade said. "The morale of troops remain high."
Boko Haram's stated goal is to bring its extreme, twisted version of Sharia law to the masses. In the process, it's brought terror -- attacking churches and mosques, bombing crowded markets and raiding once peaceful villages, even kidnapping people young and old, most famously the more than 200 girls taken last April from a school in Chibok.
And given its location along Lake Chad in Borno State, about 110 miles north of the state capital of Maiduguri, Baga has frequently found itself in the middle of this violence.
This reached a bloody crescendo in early January, when Boko Haram stormed Baga and surrounding towns in what Amnesty International said
"could be Boko Haram's deadliest act
The Islamist militants sprayed bullets as they stormed the area in trucks and armored vehicles, according to local authorities. Some stopped only to hop onto motorcycles and chase residents who had fled into the bush, firing indiscriminately, said Baba Abba Hassan, a local district head
Local officials reported death tolls ranging from hundreds to as many as 2,000 people.
"Dead bodies litter the bushes in the area and it is still not safe to go and pick them (up) for burial," Musa Bukar, the chairman of the local government where Baga is located, said then.
"Some people who hid in their homes were burned alive."