One thing to note is that container shipping fundamentally changed the definition of what is a good port -- now you want someplace with large, flat areas behind the port to park the container farm. You don't need to be in/near town since those containers are getting onto trucks and trains not getting manpacked into markets in town. On the flip side the ships are much, much larger and much hardier. Large enough that they will oftentimes weather storms at sea rather than need a protected harbor. And definitely too large to go up many rivers.

In pre-modern times your port had different functional requirements. First, a protected harbor was very, very important as ships were smaller and lack of engine power makes weathering storms at sea much more challenging. Second, the ships were small enough to use rivers effectively. Third, moving goods overland is much harder so getting the port closer to the people makes more sense.

In the cases you give these ports aren't many miles from the coast effectively -- they are a few miles upriver from the coast on what were, at the time, easily navigable great rivers. In Bruges case the river access was opened by a storm in the 12th century. By the 1500s the same channel had started silting and the trade moved down to Antwerp -- another Flemish city on a bigger river but not directly on the sea.

I can't speak to Bristol, but with regards to Bruges and other Flemish ports, the answer is quite simple: the Flemish coastline used to look drastically different to what it looks like today and was subject to heavy human-induced and natural changes throughout the years. Heavy floods, changing sea-levels, the destruction of the dune ecosystem by human encroachment, the construction of harbours and dykes, etc all had their impact.

A good example of this is Ostend, which was originally constructed on a small island called Testerep off the coast of Flanders, along with Middelkerke and Westende. Although the town bloomed throughout the 13th century, it was partially built on dune land and the dykes meant to protect it were poorly maintained. Come the Saint Clemens flood of 1334, parts of the town were submerged and had to be rebuilt. After the Saint Vincentiusnight of 1394, it became clear the town couldn't survive another flood - so it was moved further south, away from Testerep and behind sturdier dykes. Eventually, the entire island slowly sank beneath the waves, following the Saint Felix flood of 1530.

Bruges used to have a direct connection to the sea, being a coastal settlement during late antiquity. As the sea retreated, however, Bruges remained connected to the sea via various inlets. The main inlet turned into Het Zwin after the storm surge of 1134, opening up access to the city even further. It's worth noting, however, that while Bruges still functioned as a port at this point, the city of Damme was constructed during the 13th century as a sort of pre-port to Bruges. Large ships weren't able to get through the final stretch to Bruges, so Damme was built so they could transfer their cargo to barges which could reach Bruges itself. Bruges' infrastructure, reputation and connection to inland trade routes guaranteed its relevance for the time being.

Subsequent floods would not be as benefitial, however, as throughout the 12th and 13th century (and onwards) the dunes that shielded Flanders from the worst of the storms and the floods were encroached upon, mainly for exploitation as grazelands. The growing demand for meat, leather and butter in the emerging cities, as well as the financial gain to be had from doing so, led to the counts opening up the dunes and although strictly regulated at first, by the 14th century these regulations were barely enforced and the dunes were irrepearably damaged and had lost their function as a sea barrier.

The results were pretty catastrophic and most of note to Bruges was the loss of Wulpen, an island at the end of the Scheldt estuary and Het Zwin, north of Cadzand. You can see it on this map - Bruges is just off-map south of Damme:

http://i.imgur.com/uTzSRRE.png

(that's a different Oostende and Westende than the ones I mentioned earlier, by the way)

Wulpen was lost to the Saint Elisabeth Flood of 1404, slowly being washed away over the next century and cutting off a significant part of Het Zwin. The new estuary mouth of Het Zwin was now much narrower, reducing the eroding effect of the tidal flow. This led to the silting up of the water course, made worse by the development of sand banks in the area. Economic decline and political instability led to the city being unable to reverse this evolution. The coastline, meanwhile, was stabilised by the construction of various dykes (most notably the Graaf Jansdijk) and polders, leading to the current situation where Bruges is about 15km from the shore.

To sum up: the shifting of the shoreline due to natural and human intervention throughout the years have led to some historic port cities being somewhat oddly located to modern eyes.