The Ministry of Defence (MoD) has submitted plans for the Faslane naval dockyard to pour more liquid waste into the Gareloch as the number of UK nuclear subs based there rises from five to 14 by 2019. The waste comes from the subs' reactors and includes radioactive cobalt-60 and tritium.
The MoD also wants to keep emitting tritium gas into the atmosphere from the nuclear weapons stored at Coulport on Loch Long. Annual emissions of tritium have doubled between 2008 and 2012, and are expected to rise with the introduction of upgraded warhead designs.
Proposals to shift some submarine work to Coulport will also mean radioactive waste being transported by road between the two bases.
The MoD said all discharges will be within authorised limits. But critics said the Scottish Environmental Protection Agency (Sepa) and the Scottish Government should crack down on the pollution. Sepa is under pressure to delay giving the go-ahead to the increases until it has been given the tough new statutory powers promised by the Scottish Government last week.
In the wake of the MoD's failure to reveal a 2012 radioactive incident at the Vulcan naval reactor in Caithness, the Scottish Environment Minister, Richard Lochhead, last week promised to end the MoD's Crown immunity from regulation on radioactive pollution.
"This is not the time for an informal gentleman's agreement," said John Ainslie, co-ordinator of the Scottish Campaign for Nuclear Disarmament. "After being bullied by the MoD at Vulcan, Sepa should wait until the Scottish Parliament gives them full power." Then they should set legally enforceable limits for discharges, he argued.
The Sunday Herald reported last week that the Scottish Government planned to send all 14 nuclear-powered submarines - not just those equipped with nuclear warheads - back to England if Scotland votes for independence in September.
Glasgow's Green MSP, Patrick Harvie, called on Sepa to challenge the "environmental arrogance" of the MoD. "We must give our regulator the teeth to get stuck in when necessary," he said.
Sepa pointed out that under the proposed voluntary letters of agreement with the MoD, high discharge limits for radioactive waste from Faslane and Coulport would come down. But it said that the actual discharges would increase as the number of submarines rose.
A spokesman said: "Sepa plans to continue the determination on proposed changes to the existing agreements. Following this determination there is a further consultation period with relevant stakeholders, including Scottish Government, before the final decision to change the agreements."
The MoD did not comment on the planned increase in radioactive discharges. It had proposed reducing the discharge limits, said an MoD spokeswoman, who added: "Her Majesty's Naval Base Clyde continues to operate safely and there is no safety risk to the public."
Defence Secretary Philip Hammond clarified his remarks about the January 2012 radiation incident at the Vulcan reactor in Caithness, saying he had meant to say there was "no measurable change in the alpha-emitting particulate discharge" from the site. But Sepa said no such discharges were permitted so they should "always be zero".