The two ancient human skeletons were dug up from sites being prepared by Anglian Water for new large-scale water pipelines.
Both sets of bones, which were uncovered in separate archaeological exploration sites near Navenby, are believed to be from the Iron Age.
Other items, including parts of small buildings and fragments of pottery, also believed to be from the Iron Age, were found.
The work is part of a huge 25-year drive to secure future water supplies across the Anglian Water region.
Up to 500 kilometres of new, interconnecting pipelines are being planned by the water company to allow water to be moved from areas where it is more plentiful in north Lincolnshire to areas of scarcity in the south and east of the region. It is the biggest water infrastructure programme for a generation and will greatly reduce the number of homes and businesses relying on a single water source.
Construction on the first section, which runs from Lincoln to Grantham, is due to begin this Spring.
James Crompton, Direction of the Strategic Pipeline project for Anglian Water, said: “Our work does occasionally mean we discover historical remains and artefacts, which is both exciting and important.
“We recognise the immense value of finds like this and will always work with experts to handle the discoveries in an appropriate manner. We care about the areas in which we are working and will always be respectful of anything we find.
“Our new network of water pipelines will boost resilience for dozens of communities and keep fresh, clean water flowing across our region. But these discoveries serve as a reminder that our work is much more than that, and we have an important social and environmental role to play.”
Archaeological excavations were being carried out on the sites because they are known to be rich in history from different periods, including the Viking and Roman era.
Environment and Heritage Assessor for Anglian Water, Jo Everitt said: “We know that Iron Age communities existed in the area around Navenby, and that there is well-defined Roman history there too.
“The main Roman road running from London to Lincoln and on to York, Ermine Street, now known as High Dyke, runs parallel to the proposed Lincoln to Grantham pipeline.
“Such discoveries tell us a lot about our ancient history and how Iron Age communities experienced day to day life. They can also help enhance our understanding of the development of our regional and national heritage.”
The skeletons have been sent for further analysis by Trent and Peak Archaeology and Oxford Archaeology East, who carried out the excavations.