There's not some single set of major changes historians have to know, different historians deal with different topics, time periods and regions. But for instance here in Sweden and in the Nordic countries in general you have to deal with post-glacial rebound. Like a very big, very slow cork, the land is rising after having been pushed down into the Earth's core during the last Ice Age by the sheer weight of the ice. The rate of rebound depends on where you are but here in the Stockholm region it now amounts to about 5mm a year, which is significant. So for instance Karl XI's fishing cabin (google street view which was once built at the very water's edge in the late 1600s, is now over 130m from the water. During the Viking Age, when recorded history in this region starts, the shoreline was 5-6 meters higher and this is something that must always be taken into account considering geography not least since waterways was the main form of transportation. So for instance, the ancient religious and political center at Uppsala was once at the mouth of the Fyris river, but due to the land rising a new port town named Aros (meaning river-mouth) emerged 5 km south of it and by the 13th century took over as "Uppsala" (Uppsala now termed Old Uppsala). Yet today, central Uppsala is another 5km from the river mouth, which is another suburb named Flottsbro. Likewise, there are significant inland waterways that were important in the Viking Age (such as Långhundraleden) that were lost. Where longships once sailed, there is now barely more than an irrigation ditch in a field. It was forgotten, and it was not until the 20th century that Långhundraleden (which is a modern name) was rediscovered and explained a lot of archaeology.

The very location of the Swedish capital is in no small part a consequence of this geological fact; the läke Mälaren, one of the largest in Europe was once a bay of the Baltic Sea, but was transformed into a lake by the land rising in the 13th century, at which time Stockholm was founded at the threshold where the lake meets the sea. There many places on the mainland with names like "Lily island" (Liljeholmen) or "Mill island" (Kvarnholmen) or "Blasius' island" (Blasieholmen) from former islands that are now just hills or elevated areas. So many in fact that nobody even gives such incongruous names a second thought. We're simply accustomed to things being named islands while being well inland.

So in short though, post-glacial rebound is one effect htat must be taken into account if you're studying anything to do with historic coastal geography here in the Nordic countries.

Over a historical (let's say 5000 years) timescale the biggest change to consider would probably be changing sea levels, the course of rivers, tidal areas, and erosion by water. Really water in general is going to be the cause of most changes in that geologically short time frame.

This has man-made and natural causes from climate change, drainage can reclaim land but can also lower the ground level as it dries out. Sea levels change and coastlines erode and shift. These are usually quite maegi al changes and so their effect is more pronounced in marginal areas such as the Netherlands or the East of England where small changes are often the difference of a tidal marshland and flat but dry solid ground.

That time scale is also enough for rivers to move as they erode new courses. Also many rivers are managed or canalised in more recent history to stabalise their course, but this I unlikely to have their only course.