Error had won the brief after a competitive pitch against a final shortlist of four agencies.
The site, which was last redesigned in 2008, receives an average of 166,000 visits a month.
Web manager Lisa Jones said: “We started from scratch with the aim to create a website design that was going to serve our users and visitors better.
“One of the challenges our designers faced was bringing together all these different museum and gallery brands under one central ‘National Museums Liverpool’ brand, while keeping the strong identity of each venue.
“We think that the talented team at Error have provided a solution to this.”
The new, responsive site is built in HTML5 and uses Google Translate to allow visitors to read the site in a variety of different languages.
Error had worked with National Museums Liverpool before, building an online map as part of the Mapping Memory project with the University of Liverpool and Re-Dock. Other clients have included DaDaFest and St John’s College in Cambridge.