The inaugural Northeast Conference women's swimming championship was dominated by first year NEC member UMBC, which played host to the competition.  The Retrievers won 14 of the 20 contested events, including a sweep of the relay and diving events.  CCSU captured the other six events but came in third behind St. Francis (PA).  UMBC took home its second straight crown in 2000, narrowly edging out CCSU, 727-678.  CCSU's Olga Budasz was named the meet's Outstanding Swimmer for a second consecutive season.  In an exciting meet in 2001, CCSU won the final event to dethrone UMBC by a mere four points.  CCSU's Tammie Repass became the third straight Blue Devil to earn Outstanding Swimmer honors.  UMBC stormed back to win the 2002 championship, but it was CCSU's Budasz who reclaimed Outstanding Swimmer accolades.  UMBC won for the fourth time in five years in 2003, while CCSU's Repass garnered Outstanding Swimmer honors for the second time in her career.  In the summer of 2003, Florida A&M, Georgetown, Georgia Southern, Gardner-Webb, North Carolina A&T and Radford joined Howard as associate members in women’s swimming. Joining Howard as men's swimming associate members were Florida A&M, Georgetown and VMI.  In its inaugural season, Gardner-Webb won the 2004 NEC championship behind the performance of Terra Wilson, who was named Outstanding Swimmer after earning five gold medals and setting three meet records.  Gardner-Webb repeated in 2005, with star swimmer Taylor Simpson going on to be named a first team ESPN The Magazine Academic All-American at year's end.  Garnder-Webb made it a three-peat in 2006 as Simpson earned her second straight first team Academic All-America nod.  In its final year as an NEC associate member, Gardner-Webb won its fourth straight league crown led by Terra Wilson, who won her second straight Outstanding Swimmer award, then went on to become the NEC's first NCAA All-American following a sixth place finish in the 200 freestyle at the national meet.  CCSU won its first league championship in seven years in 2008, then repeated in 2009 with a close win over Wagner.  Saint Francis U earned a spot at the podium in 2010 with its first-ever NEC title, then repeated in 2011, 2012 and 2013 to match Gardner-Webb's league record of four straight crowns. Wagner won its first NEC championship in 2014, and with 844 points, became the first team to break the 800 barrier since 2003 and only the fourth team since the first championship in 1999. CCSU edged Wagner in 2015 to win its fourth NEC title, then repeated in 2016 and 2017. Bryant led wire-to-wire to win the program's first NEC championship in 2018, defended its title in 2019, three-peated in 2020 and became just the third school in conference history to win four straight in 2021. In 2002, the Bulldogs became the first team in league annals to make it five straight, rallying to beat CCSU on the final day. The Blue Devils made it back to the top in 2023, winning a seventh NEC title, then repeated in 2024 with a record-breaking point margin. CCSI three-peated in 2025 and won its ninth overall championship.

CCSU's Jaime Crowley competed at both the 2005 and 2006 NCAA Swimming Championships.  She also took part in two events at the World Championship trials in Indianapolis in 2005, and along with teammate Lindsey Snyder, competed at the 2006 U.S. Spring Nationals.  CCSU's Juliana DiPlacido was named NEC Outstanding Diver three straight years from 2004-06 and Bryant's Casey Ostrander was tabbed NEC Outstanding Swimmer four years in a row from 2010-13. Wagner won its first NEC championship in 2014, and with 844 points, became the first team to break the 800 barrier since 2003 and only the fourth team since the first championship in 1999. CCSU edged Wagner in 2015 to win its fourth NEC title. In 2015, Wagner's Anu Nihipali became the first NEC swimmer since 2007 to compete in the NCAA Championships.