Charlie Dunn, from Tamworth, was found submerged in a paddling area on a visit to Bosworth Water Park, Leicestershire, on 23 July last year.
Lynsey Dunn, 28, and Paul Smith, 36, also pleaded not guilty to a separate child cruelty charge at Leicester Crown Court.
A trial is set to begin at Birmingham Crown Court on 29 November.
The pair are accused of causing the death of Charlie by gross negligence by permitting him to enter a bathing area unsupervised.
Both defendants, of Caledonian, Glascote Heath, Tamworth, also denied four other child cruelty offences relating to three other children.
The five child cruelty offences are alleged to have taken place between March 2012 and July 2016.
Mr Smith, who appeared via video-link from HMP Leicester, also denied two charges of witness intimidation, where he is alleged to have threatened the father of one witness and threatened to petrol-bomb the house of a woman's family.
He is also accused of telling the woman he would "rip her head off".
Mr Smith remains in custody, while Ms Dunn has been released on bail ahead of the trial.
A further directions hearing is due to take place at Leicester Crown Court on 20 October.
The mother and stepfather of a five-year-old boy who drowned in a lake have denied his manslaughter.