Rotunda Museum, Scarborough

Scarborough's revamped Rotunda has long been near the top of my must-see museums list, and as news of the proposed structural changes to this tiny but hugely important 1828 building gradually leaked out, I feared the worst.

Opened by the Scarborough Philosophical Society in 1829, the Rotunda project was essentially the brainchild of William Smith, the "father of English geology", and was designed to illustrate and communicate his geological principles, particularly as they related to the North Yorkshire coast.

The original building, which is effectively a diminutive reworking of Donato Bramante's Tempietto in Rome, acquired additional single-storey wings in the 1860s, but between then and the building's closure at the end of 2006, very little was added: indeed, the lavatories were still in the back yard.

The displays were a rather different and sadder matter: over the years the geological, archaeological and natural science collections were dispersed; by the middle of the last century they had been replaced by a mishmash of exhibits deemed appropriate to a museum which is, to all intents and purposes, on the beach.

What remained, however, was the wonderful first-floor gallery with its original curved floor-to-ceiling Regency cases, its eccentric travelling platform serving the upper displays and its encircling geological diorama of the Yorkshire coast.

Access was via a central spiral staircase, so that the visitor effectively rose up through the floor of the world into the emerging clarity of the domed space above. It was a moment of quiet but perfect drama, but it was a moment incompatible with the demands of universal access.

So out has gone the original staircase, in has come a central glass lift shaft with a hideously intrusive, clunky and anything-but-transparent lift, flanked by a modern staircase that decants you into an overwhelming sea of blood-red lino (symbolising magma, perhaps?) and gone, too, is that wonderful moment of spine-tingling revelation. But are there compensations for this architectural vandalism?

Indeed there are, and they are many. To begin with, the newly landscaped approach to the museum has rescued it from the former horrors of random municipal planting and allowed for easy access and a new ground-floor entrance in the original basement. The restored external stonework glows golden and the entrance signage is as near perfect as it gets.

Once inside, the Rotunda Museum's new identity is immediately clear: it is now the William Smith Museum of Geology, whose mission is to tell the story of itself and its collections and to introduce visitors to the fascinating story of geology. And, with very few reservations, it does its new job brilliantly.

If you take the lift straight up to the top floor - though it's still better to go via the new staircase if you can manage it - the staff and designers have managed to reinstate if not the founding displays, then at least what must have been their spirit. As the nicely produced free booklet states, the displays pay "homage to the vision of the Scarborough Philosophical Society and to Smith's ideas".

Cases such as Scarborough Collectors, Yorkshire Geologists, Women Collectors, Maps and Museums, Scarborough Inventors and William Smith's Big Idea, anchor the visitor in the locality and introduce the anything but parochial ideas of the time. There is, predictably enough, a display on the development of Scarborough as a resort, but it too is centred on the area's geological foundations.

There's quite a lot of in-case reading to be done, but somehow it doesn't seem too challenging and it's perfectly possible to get to grips with basic facts via the information plinths in front of each section, despite the fact that a number of the "books" are already broken. I particularly liked the judicious use of quotation and the peopling of the gallery with original and reproduced portraits.

Downstairs, in one of the 1860s wings, is the Shell Geology Now gallery, in which you can name your own fossil, "meet the geologists" on screen, learn how to engage in a bit of DIY geology without damaging vital scientific evidence and understand just why the museum's collections are so important.

Interactives are fun and informative: were I in charge of decisions about coastal defences, we'd all be doomed within a decade or two.

The star of this gallery for me is the presentation of 4,000-year-old Gristhorpe Man, who was unearthed in 1834. Beautifully and accessibly unravelled, though not in the least dumbed down, is the story of archaeology's 200-year development from a gentlemanly art into a 21st-century science.

Particularly revealing are comparative 1843 and 2008 labels for the same objects. The other wing offers the Gateway to the Dinosaur Coast, Scarborough Museums Trust's ongoing collaborative regional project.

Although aimed primarily at younger children, its mission is to get everyone out, discovering and understanding this fascinating coastline. The colourful design is redolent of early 20th-century railway posters, there are lots of pull-out specimen drawers and there's plenty of encouragement to the best kind of family tourism.

There's a small but appropriately stocked shop in the reception area, the new lavatories are well-tended and, furthermore, indoors. The staff couldn't have been more helpful and more obviously proud of the museum.

The price for all this has been the partial loss of an architectural gem, but it was a gem that was already sadly debased and, for the many first-time visitors, it's a loss that won't be felt.

Instead, what they will encounter is a gem of a different kind: an all-too-rare example of a small but almost perfectly formed local museum that is sure of its purpose, confident and generous in its expertise and focused not on ticking boxes but on inspiring its audiences.

Nichola Johnson is the director of the Sainsbury Centre for Visual Arts at the University of East Anglia