While implementing design works for the future museum, a drawing of 1929 was found in the Water Tower at the Main Water Works with the inscription: "Former museum building". It means that the museum existed in this building before. After the long archive search it was found that the proposal of E.A. Ganneken, Head of Water Pipelines, to create a special museum was reviewed during the technical meeting of St. Water Supply Company on November 8, 1900. The museum should have been "a help for water network development and better illustration of history and state of water supply activity in terms of operation in the capital". In the exhibition it was supposed to collect samples of different items used for build and operation of water pipelines; samples of unusual damages at the networks and pipelines operation; sample, methods of water treatment, drawings, models, machinery and also "everything related to the history of creation and operation of water pipelines in St. Petersburg in general".

On 11th of June 1901 S.P. Pyata, Chief Mechanical Engineer, represented "a short list of manuals and patterns which are desirable to be in the museum" in order to popularize water business, to train new and young technicians and students of some educational institutions visiting the Main Water Works on annual basis" to the Head of Water Pipelines.

On the 12th of June at the meeting of the City Executive Commission for Water Supply Mr. Ganneken, Head of Water Pipelines, offered to locate a museum on the third floor of the Water Tower (from the beginning of the ХХ century it has not been used for its direct purpose).

On the 19th of January 1902 Mr. Ganneken gave an order to the Chief Mechanical Engineer "to take measures in order to prepare the building intended for the museum of St. Petersburg Water Pipelines by February of this year". Next year four cabinets, four showcases, a writing desk and a desk for drawings were in the list of the museum property. The documents confirming continuous refilling of the museum collection can be found in the archives. When Mr. Genneken, Head of the Water Pipelines, retired in 1910 the correspondence related to the museum was reduced and then it was stopped completely in a year. It is only known that in July of 1911 the Technician R.I. Khmelevski took the responsibility for the museum instead of the Engineer R. Rose.

In 20s – beginning of 30s of the ХХ century the city Museum of housing and utilities infrastructure with a section dedicated to water supply and wastewater disposal was situated in Anitchkov Palace (then the Palace of Pioneers was opened there). Nobody knows where the exhibits of the former city pipelines museum disappeared. They could not be found in St. Petersburg museum funds...

New exhibition "The Water World of St. Petersburg" was opened in the Water Tower in 2003. In the left extension of the Tower one more exhibition "The Underground World of St. Petersburg" appeared.

At the International Forum of European Museums held in May 10-14, 2006 in Portugal, the Water World of St. Petersburg was marked very high for "its great achievements in the raising of social significance of museum collections". The museum officially represents Russia in the European Association of Water Museums.

In five years after the starting of the museum work in the Water Tower, Vodokanal of St. Petersburg opened one more museum exhibition in 2008 – "The Universe of Water". The first visitors were able to get familiar with the exhibition when Vodokanal celebrated its 150th anniversary. "The Universe of Water" is also situated in the industrial building - in the former clean water reservoir of the Main Water Works.

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