Having broken her short course 100m British Record last week in Sheffield, the 16-year-old repeated the feat in the long course pool clocking 1.00.99 for gold.
S14 swimmers Chloe Davies and Natalie Massey finished second and third respectively in 1.04.41 and 1.04.45.
Paralympic Champion Jonathan Fox claimed gold in his main event as he set 1.11.14 for victory in the MC 100m Backstroke.
The S7 swimmer said: “I’m really pleased with that race. It was a second faster than I went in Swansea recently so things are looking good for the World Championship qualifications.
“I’m trying to focus on the 400m Freestyle and the 100m Backstroke at the moment. Unfortunately I lost my 400m Free record in London so I want to push to get that back but Backstroke has always been my best really.”
James Crisp (S9) claimed silver in 1.05.00 while S14 Jack Thomas took bronze in 1.06.57
Hannah Russell won her first gold of the meet in the MC 100m Backstroke. The Paralympic medallist set 1.10.00 for gold ahead of Applegate and Davies who touched in 1.09.35 and 1.10.18 respectively.
She said: “I’m really happy with my race. It was definitely a big improvement on this morning.
“I was just off my personal best pace but I’m still really pleased. Having two back to back swims is hard and a lot of us were in the same boat but I just tried to pretend it was like training where we do max swims with a short rest.”
Dan Pepper was victorious in the men’s MC 100m Freestyle. The S14 swimmer finished in 56.42 to hold off his training partner and fellow S14 Ben Procter in 56.53.
Third place went to S7 swimmer Josef Craig in 1.02.86.