Charlie Dunn, from Tamworth, died in hospital after being found submerged in the Blue Lagoon area at Bosworth Water Park in Leicestershire on 23 July.
Lynsey Dunn, 28, and Paul Smith, 36, who are believed to be the boy's mother and stepfather, have been charged with manslaughter by gross negligence.
They are also accused of seven child neglect offences.
These offences are alleged to have taken place between April 2012 and July 2016.
Live updates from the East Midlands
In addition, Mr Smith has been charged with two counts of witness intimidation alleged to have taken place in March 2016 and June 2017; one count of threats to damage or destroy property by fire in June 2017; and eight driving offences which are alleged to have taken place in January and June 2017.
Both defendants, of Caledonian, Glascote Heath, Tamworth, appeared at Leicester Magistrates' Court earlier and are due to appear at Leicester Crown Court on 5 July.

Japan should learn "profound lessons from history", China's defence ministry said after Japan's parliamentary vote.
The vote allows Japanese troops to fight overseas for the first time since the end of World War Two 70 years ago.
Tensions between China and Japan have escalated in recent months over a group of islands to which both lay claim.
The security laws were voted through Japan's upper house late on Friday, with 148 lawmakers voting in support and 90 against.
It followed nearly 200 hours of political wrangling, with scuffles breaking out at various points between the bills' supporters and opposition members attempting to delay the vote.
Compiled by BBC Monitoring
The government says that the changes in defence policy are vital to meet new military challenges such as those posed from a rising China.
But China's defence ministry said on Saturday they "run counter to the trend of the times that upholds peace, development and co-operation", the Xinhua news agency reports.
"The move has breached the restrictions of Japan's pacifist constitution," the ministry added.
Many Japanese who opposed the bills - which prompted large public protests - were also attached to the pacifist provisions in the constitution that banned fighting overseas.
China also urged Japan to "heed the security concern" of its Asian neighbours and do more to promote regional peace and stability.
South Korea, which also has a tense relationship with Japan, has warned Tokyo not to exercise the new defence laws without its approval.
But the US, Japan's ally, and the UK have both welcomed the changes.
UK Foreign Secretary Philip Hammond said he looked forward to Japan "taking an increasingly active part in peacekeeping operations".
Japan's post-World War Two constitution bars it from using force to resolve international conflicts except in cases of self-defence.
The new security legislation allows Japan's military to mobilise overseas when these three conditions are met:
What's behind Japan's military shift?
Critics say the changes violate the pacifist constitution and could lead Japan into US-led wars abroad.
Supporters of the measures insist they are essential for the defence of Japan and its regional allies, and will permit greater involvement in peacekeeping activities around the world.
Critics have focused on what they say is ambiguity in how the principles of the legislation will be interpreted, and the possibility that future governments will interpret them more broadly.

The 18-year-old will provide cover for Luke Daniels, who starts a three-match ban for his red card in the opening day defeat at Burton on Saturday.
Watson, who is yet to make his Tigers debut, could feature for the Iron in Tuesday's League Cup tie with Barnsley.
He tweetd: "Delighted to have joined Scunthorpe on a month's loan. Looking forward to getting started tomorrow."
Find all the latest football transfers on our dedicated page.

He had an initial spell with the Vikings between 2008 and 2013 and was named one of its 50 greatest players.
Defensive end Allen, 34, last played for the Carolina Panthers in 2015 and also had spells with the Kansas City Chiefs and the Chicago Bears.
"We are proud to have Jared retire as a member of the Vikings franchise," said Vikings owner Zygi Wilf.
A man and woman have been charged with the manslaughter of a five-year-old boy who drowned in a lake.
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China has said Japan is endangering peace in the region after it passed controversial laws expanding the role of its military abroad.
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Scunthorpe United have signed Hull City goalkeeper Rory Watson on a 28-day emergency loan.
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Jared Allen will retire as a Minnesota Vikings player after he signed a one-day deal with the NFL team on Thursday.