Lawyers for Wright previously argued the EA only had the power to bring private prosecutions for environmental offences, not fraud or conspiracy.
But EA barristers said it had a general power to bring private prosecutions, and alternatively that allegations of conspiracy to defraud were connected to its functions.
Massey, Gregory and Barker did not appear at the hearing in London and were not represented.
Lord Justice Popplewell, sitting with Mr Justice Hilliard, ruled on Wednesday that the EA only being able to prosecute environmental offences would “produce unreasonable and anomalous results”.
He said the law “enables the EA to prosecute for any offence of any nature in circumstances in which such a prosecution is capable of being calculated to facilitate, or conducive or incidental to, the carrying out of any of its functions”.
In the 48-page judgment, he said the charge against Wright involves “very serious allegations of criminal misconduct”.
He said: “What is alleged … involves carefully planned and extensive fraud and dishonesty at a high level within the company and on a large scale, including, for example, arranging for wastewater to be removed from facilities by tankers in order to create no flow results, with a view to covering up pollution and deceiving those whose function is to protect the public from such harm.
“The EA says that by the company’s own assessment, it avoided penalties of the order of £45m, and on the EA’s assessment the figure is higher.”
Following the judgment, an EA spokesperson said: “We can confirm that we are taking criminal proceedings against Southern Water Services Limited and a number of former employees.
“We take our responsibility to protect the environment very seriously and will always pursue and prosecute those alleged to have committed serious offending against the environment. We welcome this important judgment.”
Three people have also been charged with failing to comply with or contravening an environmental permit condition.
Terry Stephens, 68, of Waterlooville, Hampshire, is charged with one count, alleged to have taken place in 2015.
David James, 60, of Worthing, West Sussex, is also charged with one count, alleged to have taken place in 2016.
Mark Butler, 47, of Hassocks, West Sussex, is charged with eight counts, alleged to have taken place between 2015 and 2024.