In 1990 the founders of the Spring Island Trust recognized that the quality of life on Spring Island would be significantly diminished if the surrounding area was heavily developed and/or the waters became polluted. The Trust was a tax-exempt organization (501(c)4) but not a tax deductible nonprofit, so the LowCountry Institute was founded in 1998 as a 501(c)3 tax-deductible organization to serve as a partner to the Trust, conducting environmental outreach throughout the Lowcountry region for 18 years. During that time LCI became recognized regionally as an important source of accurate environmental and ecological information. LCI was able to guide Beaufort County Council and local municipalities to support stronger stormwater guidelines and protect critical open space. LCI also established the Master Naturalist program and the Coastal Kingdom TV series.

In 2016, the Spring Island Trust received tax-deductible status and the Trust and LCI were merged the following year. The LowCountry Institute now exists as a tradename of the SIT. To ensure that successful LCI programs continued, the bylaws of the new organization established the LowCountry Institute Advisory Panel. Its purpose is to ensure that regional outreach continues to be an important part of the Trust’s activities. This panel reviews staff recommendations and makes formal proposals to the Trust board for research projects and outreach programs. Examples of ongoing outreach programs are Master Naturalist and Coastal Kingdom. Research programs typically fall into two categories: projects that help the Trust more effectively manage its nature preserves and projects that increase our understanding of what is required to protect water quality and marine animal populations in the Chechessee and Colleton Rivers.