The southern part of the church is of a later date and shows several incongruous features. It seems clear that during the 15th century the whole of the southern part of the church was rebuilt. A lot of older pieces were used again but many of them are not in their proper places making this part of the church is a curious architectural muddle. The arches between the nave and the south aisle are of about 1250. The pillar by the font is interesting for its cluster of columns round a concave core, a design copied from pillars in Lincoln Cathedral. The font itself is also from about 1250, though this has been damaged and at some time has been partly buried in the ground.
In the Lady Chapel there is a tomb recess, though this is an example of older material being reused for there is no tomb there now. Behind the altar, along the east wall of the chapel, is a fine frieze of carved stone, possibly Norman. On the floor is a good 15th-century brass of a priest in a cope on which is a pleasant oak-leaf motif. There is a picture of the Madonna and Child by 17th century Italian artist, Carlo Dolci. The picture was given to the church by the RAF in 1946.
Fiskerton has received international archaeological attention on a number of occasions over the last two centuries following discoveries of Iron Age artefacts buried in the fenland peat that surrounds the village. In 1826 a fine, metre-long decorative shield was discovered in the River Witham. Now known as the Witham Shield it has been dated to 400-300 BC and is in the British Museum.
Over 150 years later when a dyke was being cleaned, a series of posts were found together with an early to mid Iron Age sword. Subsequent excavations in 1981 revealed the posts to be a wooden causeway which dendrologists dated to a period between 457 and 300 BC. It appeared to have been repaired and added to every eighteen years or so during that period and the construction and maintenance of a walkway on such a scale at that time would have been a major feat of engineering. Hundreds of artifacts were also found around the causeway, including eleven spears, six swords, woodworking and metalworking tools, as well as part of a human skull which had a crescent-shaped chop mark, probably inflicted by a sword; this injury is unlikely to have killed the man. (Field, Naomi and Pearson, Mike Parker, 2003. Fiskerton: An Iron Age Timber Causeway with Iron Age and Roman Votive Offerings, Oxbow Books, Oxford). Twenty years later in further excavations more sections of the causeway were dug out, some of them containing posts several metres long, plus a complete spear, a currency bar, a sword, a dagger, some bronze fittings and the icing on the cake, two Iron Age boats. One of these boats as well as other artifacts can be seen at The Collection in Lincoln. The area around the site of the causeway, which is alongside the road to Short Ferry, (a hamlet 2.5 km to the east) opened as a nature reserve managed by the Lincolnshire Wildlife Trust in 2006.
During the Second World War, an airfield was built on agricultural land to the north of the village. RAF Fiskerton opened in January 1943 as part of 5 Group, Bomber Command as 52 Sub-Base Station controlled by RAF Scampton. It closed at the end of the war in September 1945 and the land returned to agricultural use. Very little can be seen of the old airfield now, but a memorial to No. 49 Squadron RAF and 576 Squadron, who were stationed at the airfield during the war, can be found by the side of the road between Fiskerton and Reepham, a village 2.5 km (1½ miles) to the north.