Marvelly's role, which she took up in July last year, was to oversee the exhibition development project while a separate project team was responsible for the strengthening of the museum building, now scheduled to open in 2025.
The council said Marvelly "led the museum through the early stages of exhibition development and community engagement, and spearheaded the development of a new strategic direction".
Rotorua Lakes Council chief executive Geoff Williams acknowledged Marvelly's impending departure.
"Lizzie has been an asset to the museum, bringing fresh thinking and energy. We are disappointed to see her go, but we understand that her family needs to take priority at this exciting time in her life.
"We thank Lizzie for her service to Rotorua Museum Te Whare Taonga o Te Arawa, particularly through the challenging time of Covid-19. We wish her all the best for her future endeavours."
Asked if council would be recruiting to fill the position, Williams said: "We are working through what needs to happen now and will share details once all is finalised."
Te Pukenga Kōeke o Te Whare Taonga o Te Arawa chairman Monty Morrison said he was "disappointed" but understood her reasons for stepping down.
"Of course her impending motherhood is where she will need to put her efforts," he said.
Morrison said everyone had a "clear vision under her guidance" but he was confident that work would continue.
"We felt she would have been a great fit to take us forward to implement a new vision for the museum – re-energise it, give it a new focus and take us into the future.
"But that won't be lost because the work will be ongoing."
He said he looked forward to thanking Marvelly in person shortly.
The museum has been closed since November 2016 after the appearance of cracks in some parts of the building following the Kaikoura earthquake.
Construction, to strengthen and redevelop the category 1 Bath House building in which the museum is housed, was due to start next year and expected to take two years.
In June, it was announced it would receive a $4.1 million grant from the Bay of Plenty Regional Council towards the creation of exhibitions for the strengthened and redeveloped facility.
Marvelly previously said this meant planning work for the exhibitions within the museum was full steam ahead.
At the time she said they had developed a "comprehensive engagement plan" and would be talking to a wide range of people throughout the rohe.
During the community engagement programme, which was expected to take 12 months, the museum team would be gathering information from the community about the stories and taonga that were important to them, and themes they would like to see reflected in the redeveloped museum.
