Peamount United midfielder Duggan was named Player of the Season - the second time she has achieved this honour - after consistently standing out in a team that won the League and FAI Women's Cup double.
Duggan pipped club-mates Aine O'Gorman and Eleanor Ryan-Doyle, Cork City's Saoirse Noonan and Shelbourne's Pearl Slattery to the main award.
The Kilkenny native said: "It definitely is my best season in football. Winning the League last season was a monkey off our back for Peamount United, we felt like we were getting the club back to where it belonged.
"But with everything that happened this year, the group of girls that we have and finally getting our hands on the Cup trophy after many disappointments there, it was just a magnificent season.
"We really kicked on this year and it was such a tight-knit group and I'm just happy that we were able to repay all of the work that the people on the ground at the club deserve."
For the Young Player of the Season, Molloy perfectly capped off an exceptional debut season for Wexford Youths that also saw her earn two Republic of Ireland WNT caps at just 16 years of age.
She was selected ahead of Cork City's Eabha O'Mahony, Galway's Shauna Brennan, Shelbourne's Jessica Ziu and Treaty United's Aoife Horgan.
"Everything went so fast. I was just hoping to make the team in Wexford firstly and then I had a great debut and it went from there. I'm delighted that it went so well and everyone at Wexford was so good to me," said Molloy.
Duggan was also named in the Team of the Season for a record sixth time. She was joined by Peamount team-mates Niamh Farrelly, Claire Walsh, Eleanor Ryan-Doyle and Aine O'Gorman.
Shelbourne had captain Pearl Slattery and midfielder Jessica Ziu make the XI, while there was one representative apiece from DLR Waves (goalkeeper Eve Badana), Galway WFC (left-back Shauna Brennan), Wexford Youths (midfielder Ellen Molloy), and Cork City (forward Saoirse Noonan).
The four different Barretstown / WNL Player of the Month winners of Molloy, Noonan, Ziu and Duggan all made the final selection.
Awards were given to the Top Goalscorer, Aine O'Gorman, who netted 14 goals in 12 League games to win the golden boot for the third time, and the holder of the Most Clean Sheets, Rachael Kelly, who recorded five shut-outs for Shelbourne.
There was also recognition for the late Michael Hayes, who sadly passed away last September, as he was honoured with a Services to the Women's National League award.
2020 Women's National League Awards
Player of the Season
Karen Duggan (Peamount United)
Young Player of the Season
Ellen Molloy (Wexford Youths)
Top Goalscorer
Aine O'Gorman (Peamount United)
Most Clean Sheets
Rachael Kelly (Shelbourne)
Services to the Women's National League
Michael Hayes
Team of the Season
Eve Badana (DLR Waves)
Niamh Farrelly (Peamount United)
Pearl Slattery (Shelbourne)
Claire Walsh (Peamount United)
Shauna Brennan (Galway WFC)
Ellen Molloy (Wexford Youths)
Karen Duggan (Peamount United)
Jessica Ziu (Shelbourne)
Aine O’Gorman (Peamount United)
Eleanor Ryan-Doyle (Peamount United)
Saoirse Noonan (Cork City)
*The nominees & winners were selected from a voting process that was open to all WNL players & managers, along with input from a select committee.