The Spanish doctor is on trial for allegedly masterminding a wide-ranging doping ring, which has implicated athletes from cycling and a number of other sports.
Fuentes has so far not been compelled to name those athletes despite the attempts of WADA's lawyers.
However, the agency's director general, David Howman, remains confident that the truth will out.
"We worked with the UCI (International Cycling Union) on this particular case, the Fuentes trial," he told Press Association Sport.
"We have been battling away in the courts there for the last six years to try and get to this hearing.
"The first or second day, Dr Fuentes said it wasn't just cycling. He said it was boxing, athletics, tennis, football so we were right, the UCI were right to have bashed away to get to that scenario.
"We have to be patient as we go forward and wait for the trial to be completed, conducted judicially and for the judge then to make a reasoned decision on the basis of the information she has.
"We are heartened that we are before a judge that has an open mind. She has obviously understood the issues, the evidence is still coming in and when it finishes, she'll analyse it.
"We will too because some of the information we got at the trial we can think about how to use."
Football and tennis, two of the sports allegedly implicated in Operacion Puerto, have come under increasing scrutiny recently for seemingly lax anti-doping controls.
Arsenal manager Arsene Wenger believes current controls in football are not strict enough to catch the cheats and a number of high-profile tennis players have questioned how regularly they are tested.
"I think sport normally responds to controversy because nobody likes controversy," Howman said.
"The UCI have obviously had some and they have responded and are still having to respond.
"Tennis has not had a controversy but they have had their top players saying 'we want a better programme'.
"I think the response immediately was 'we'll give you one'. I think that is a good indication of commitment and we will work with tennis to see that is done.
"I recollect four to five years ago when Andy Murray was criticising the anti-doping programme for asking for his whereabouts so it is a significant shift in attitude by the top players and I applaud that. I think that is really good.
"In terms of football, it hasn't had a controversy but we have seen already in the Fuentes trial are implications that there are footballers and a few clubs involved.
"Now let's wait and see until the evidence is completed as to whether there is something can be done in relation to that information."