2000s

During 2003, local schools received police visits urging pupils to help fight crime. According to the testimony of Christoff Becker, son of Waterkloof's principal, L. Christo Becker, this served as inspiration for two coordinated attacks on loitering black men in Constantia Park and Moreleta Park during the evening of 1 December 2003. Becker and three pupils of the school, the "Waterkloof Four", displayed defiance and arrogance in court and received 12-year prison sentences for assault and murder.^[7] A fifth pupil was acquitted for testifying against them.^[8] Both Beckers believed that the trial and related incidents constituted a vindictive plot against the family.^[9]

In 2007, the school reported alleged incidents of sexual misconduct by its pupils to the police. Older boys would have sexually abused younger boys while on a rugby bus tour.^[10]

In 2008, the deputy headmaster Louis Dey (45) sued three of the school's pupils for an amount of R600,000 after an incident in 2006 where they circulated a manipulated picture of him and the principal, L. Christo Becker, which depicted them naked and engaged in a seemingly homosexual act.^[11] The three teenagers were ordered to pay R45,000 in damages for sending the image to hundreds of pupils via MMS and Bluetooth, an amount which Dey described as "shockingly inappropriate".^[12] Dey resigned his post in 2007 to assume the position of headmaster at another school when Waterkloof's pupils wouldn't stop giggling when they passed him on the school grounds.^[13]

In 2009, following a forensic audit requested in December 2008, the governing body committee stepped in to manage the school after uncovering alleged financial irregularities spanning the years 2004 to 2008, which ran into millions of rand.^[14][4] The school principal, L. Christo Becker, and his deputy, André D. Eloff, resigned before they could be put on compulsory leave. Some irate parents claimed the money was used to bankroll the protracted legal battle to keep the principal's son Christoff out of prison,^[4] while the upmarket lifestyle of his deputy was also singled out.^[7] Money was allegedly channeled through a secret account to the Aviation Academy, from which Becker took "interest free loans".^[15] The governing body chaired by Lukas Coetsee requested an audit of the Aviation Academy^[16] and considered legal steps against it,^[15] but was informed that it was an independent entity with Becker as director, and consequently not obligated to answer to them. At their hearings both Becker and Eloff implicated the governing body in channeling their "additional salaries" through the Academy.^[16] Onno Ubbink, subsequent chairman of the governing body said they were "not in a position to comment" on the department's sacking^[17][18] of Becker, Eloff and Van der Merwe, their financial administrator.^[16] A teacher speaking on condition of anonymity alleged that the improprieties could be traced back to 1999 and earlier,^[19] and that many highly qualified staff had resigned in response to their employment conditions. The same source alleged that the school's many poor pupils were not lent support, but some parents were indeed sued for outstanding fees, who had to pay legal costs as well.^[19] Leon de Beer was assigned the role of acting headmaster,^[16][15] until Daan Potgieter replaced him in 2011.

2010s

Early 2017, a married male teacher who was appointed less than a year earlier had to quit the school after his alleged intimate encounter with a grade ten pupil came to light.^[20][21] The incident of 2 February 2017 allegedly occurred in a classroom and was brought to the attention of the governing body by the principal. Its chairman disputed that the act was caught on camera or that it occurred following a "sokkie".^[22]

In April 2018 a matric boy of Hoërskool Eldoraigne and his mother visited the school to ask a Waterkloof matric girl to the boy's prom dance. A scuffle ensued between the boy and two staff members outside and inside the headmaster's office. When "urgent" interdicts were obtained against the boy and his mother three months later, the school's office declined to comment.^[23]

In early 2019 the hostel was renamed Huis Kloofsig. The hostel also introduced a new "koshuisvader", Cobus van Dyk, who was the forwards coach of the SA Schools Rugby team.

2020s

On 11 March 2020 a hacker gained access to the school's Facebook and Instagram accounts and vented anger at conditions at the school, including a supposed drop in pass rate and the behaviour of teachers, pupils and parents.^[24] In a press release headmaster Chris H. Denysschen labelled the breach as a cyber crime,^[25] but his deputy, Cobus van Dyk, claimed that the school suffered no damage to its reputation.^[26]

In February 2021 a spokesperson for the Gauteng Education Department expressed his disappointment with the disregard for social distancing at the school, even after completing COVID-19 operating procedures and regulations training.^[27] In March a grade 11 learner neglected to inform the school that they had tested positive for COVID-19, and the school placed 100 learners in isolation at a pavilion for their break times and homework session.^[28] At other times these pupils claimed to have moved about freely, but this was denied by the school's office.^[28] By April several learners and headmaster Chris H. Denysschen had tested positive for COVID-19.^[29] Denysschen recovered after a stint in intensive care.^[30]