Managers at The Deep in Hull has formally notified Hull Council of their objections to proposals for the terminal, a key part of the City Plan.
Bosses have an array of concerns from the long-term impact on the aquarium’s animals to increased traffic congestion, as well as noise and air pollution from the terminal just 260ft away.
Among the concerns is noise from engines, horns and loud tannoy announcements that could startle and stress the birds, potentially affecting their breeding patterns.
The noise of pile driving during construction has been shown to even cause “immediate death” in the wild to some fish species, experts have warned.
The Deep’s chief executive, Katy Duke, said: “It could frighten the birds which could cause them damage - they could harm each other, or run into something or fall into something. If stress builds up in them it could compromise their immune system.”
It comes after plans for a cruise terminal at Greenwich on the Thames were ditched by developers. The terminal was granted approval in 2015, but Greenwich Council pulled out over pollution concerns. Campaigners claim one ship would emit the same amount of pollution as 600 lorries.
The plans in Hull envisage cruise ships docking off Sammy’s Point, next to The Deep, which breeds some of the rarest species in the world, including the green sawfish and the Mexican walking fish.
Bodies including the World Association of Zoos and Aquariums and the British and Irish Association of Zoos have concerns over the impact on collections, which include 245 species some of which are critically endangered.
Blue Planet Aquarium also raised fears, saying aquatic species were “notoriously sensitive” to vibration and construction would “certainly pose a health and welfare risk” to penguins, as well as sharks, bony fish and octopus and cuttlefish.
The Zoological Society of East Anglia went as far as saying The Deep - “one of the best aquariums in the world” - may no longer be able to house penguins and sharks because of the impact on their welfare, adding: “This will have a major effect on your ability to attract visitors and achieve your mission.”
Figures suggest about 20,000 tourists a year will actually visit the city with 40 per cent boarding coaches to places such as York, and 20 per cent staying on board - against the 460,000 visitors to the Deep, which has a turnover of £7m and employs 160 staff.
Deputy chief executive Neil Porteus added: “We are not against the terminal if it brings in extra visitors, but we think it will displace existing visitors.
“The concern is the Deep will gain this reputation that it is difficult to get to. We wrote to the council in 2017 to set out our concerns. We have been talking to them to alleviate our concerns.
“The letter we sent (recently) was because we concluded that they weren’t taking us seriously and don’t believe those concerns could be mitigated in any event.”
The Deep prefers an alternative location at St Andrew’s Quay, where there would be ample parking on site.
Hull Council said the cruise terminal was supported by many other councils across Yorkshire and was "crucial" to Hull’s City Plan and the future development of the city centre.
The Deep had not raised objections during a lengthy public inquiry, which endorsed Sammy’s Point as the preferred location for the terminal.
It said: "The Deep is an integral part of the city and Hull City Council was a key funder and partner in its development as the UK’s most successful Millennium Project, and we remain committed to its future success.
"The Deep made no objections or representations to the Planning Inspectorate during a lengthy and detailed public inquiry on our Local Plan, which endorsed Sammy’s Point as the preferred location for the cruise terminal.
"The Deep’s Board has also been briefed regularly on how the project is developing and is aware that all of the concerns they have identified will have to be addressed as part of the detailed planning work and impact studies currently under way, and which are designed to protect and enhance their interests and assets.
"This has included working with them to develop a joint tender brief for a specialist engineering company, of their choice, to provide comprehensive acoustical testing and design mitigations to protect all aquatic species.
"The development of the Yorkshire Cruise Terminal in Hull is a hugely ambitious project, is supported by many other councils across Yorkshire and is crucial to Hull’s City Plan and the future development of the city centre.
"We are confident that we can overcome the concerns The Deep has raised.