Foyle Search and Rescue retrieved the 33-year-old's remains at approximately 11am on Wednesday.
"Our team worked closely with the PSNI and emergency services to recover his body and bring him back to his family," the rescue charity said in a statement. "Our thoughts are with Emmette’s family and friends at this time.
"We want to sincerely thank those involved in the recovery today. We want to thank our volunteers in particular, who had the difficult job of recovering Emmette’s body. We are extremely grateful for your efforts today and always. Thanks also to all emergency services that were involved.
"Finally, a special thanks to Emmette’s family, his friends and each and every person who assisted in searching; especially our own volunteers, as well as Foyle Prevention Team, Maiden City River Watch MCRW and Search Team Northwest. We appreciate all you have done this last few weeks.
"RIP Emmette Dillon."
Emmette's twin brother Ryan paid tribute to everyone who helped in the search over the past few weeks.
In an emotional Facebook post he stated: "Foyle Search and Rescue recovered Emmette today and we will finally be able to lay him to rest. It's impossible to name everyone but the outpouring of support has been unbelievable.
"I am forever thankful to you all and to all the organisations and groups who have supported us. All friends, family and work colleagues who have given their time to support us. Emmette was my twin and we had an unbreakable bond."
Anyone in distress in NI can contact Lifeline 24/7 helpline can be contacted for free on 0808 808 8000 in confidence; The Samaritans can be contacted 24/7 on 02871 265511 or Freephone 116 123 in confidence; Children can contact Childline 24 hours a day, 365 days a year on 0800 1111 for any issue or by visiting www.childline.org.uk in confidence.
Anyone in distress in RoI can contact Pieta House free on 1800 247 247 or text HELP to 51444; TEXT Crisis Textline Ireland on 50808 - a free 24/7 text service; Ring Samaritans 24/7 on freephone number 116-123,