Jon swapped Salford's Media City for Langstone Harbour in Hampshire for a special edition of the programme, exploring the issue of sewage pollution along the coastline and in our waterways.
He was joined by weather presenter Carol Kirkwood, who reported the latest weather forecast from the harbour.
Meanwhile, relief presenters Ben Boulos and Tina Daheley held down the fort in the main studio, keeping viewers up to date with the latest news headlines.
Taking to Instagram ahead of Tuesday's show, Jon posted a stunning snap of the sun rising over the harbour. Sharing details of the day's programme, he wrote in the caption: "Good morning from Langstone Harbour in #Portsmouth for a special BBC Breakfast programme about sewage and water pollution. We'll hear from the water companies, politicians, campaigners and local people."
Viewers of the show were a little divided over the subject matter of the special programme, with some complaining that it wasn't suitable for breakfast viewing. Taking to X, formerly known as Twitter, one person wrote: "Whose idea was it to do a full feature on sewage at breakfast time? Not the nicest thing when you're eating breakfast," while another added: "@BBCBreakfast How to turn viewers off from #BBCBreakfast ... talk about sewage! Bleurgh!"
However, other fans praised the show for highlighting the issue, with one person tweeting: "@BBCBreakfast special edition on sewage pollution and water quality now. Various parties being interviewed. Worth a watch," while another added: "Good morning @jonkay01 and welcome to Pompey. Thank you for highlighting just how much raw sewage is being illegally pumped into our seas."
While the reason for Sally's absence is unknown, it's possible that she took the day off for her son's first day back at school after the summer holidays.
Sally recently returned to the UK from a short break in San Sebastián, Spain. The TV star, who was missing from Wednesday's programme last week, took to Instagram on Sunday to share a carousel of snaps from her trip, including a stunning beach selfie.
"There are no prawns left in San Sebastián," she penned in the caption. "I think we have eaten them all. Back on the @bbcbreakfast sofa tomorrow from 6. Join us if you can x."
Fans were quick to react to Sally's selfie, which showed the journalist donning dark shades and a white robe. One person wrote: "Wow stunning," while another added: "Looking gorgeous."
Sally isn't the only presenter absent from the show as both Nina Warhurst and Emma Vardy are on maternity leave.
The arrival of Nina's third child with her husband Ted was announced on BBC Breakfast in July. Watch the clip below.
Meanwhile, Emma welcomed her baby boy, Jago Fionn, in August and announced the happy news on Instagram. Sharing a selfie of the journalist cradling her baby, she wrote: "Presenting my best breaking news ever. Baby boy Jago Fionn is here.
"At just a few hours old, playing a little camera shy. Huge thanks to the dedicated & talented midwives & doctors at Belfast's Royal Victoria Hospital, for looking after us so well," she wrote, adding: "Smitten & so in love."