Bay Hill Estates is the current name of the 1115 acre property originally known and still sometimes referred to as Stonewal Estates; Bay Hill Drive, the main road into the property off Northlake Blvd was originally known as Stonewal Drive. Many Palm Beach County records references are in the name of Stonewal Estates. The property has a complicated history dating back to approximately December 1983 when the original Articles of Incorporation were written and later recorded in the public records of Palm Beach County.

From 1983 through 1994 there were adverse situations that limited the development of the community. There were multiple name changes and several bankruptcies of the original developer/declarant (Tom Waldron, Supertrail, other names). Starting in 1995 lots were sold to different builders from a bankruptcy court and the community began to establish itself. In 1997 the Association individual lot owners took control of the Board of Directors. In 2000 the Association settled its legal entanglements with the original Declarant.

The original Declaration of Covenants and Restrictions was recorded in February of 1984 in Book 4158 page 205 of the Public Records of Palm Beach County for the entire property. The first description of Phase I and Phase II properties was in an amendment to the Declaration in August 1988; this amendment split the property into Phase I and Phase II and provided legal descriptions of the two properties. Phase I included 118 acres of common property, 266 acres of platted lots and 146 acres of golf course property. This amendment, among other things, allowed the Phase II owner to self-annex the property to Estates Holding, P.U.D. (a prior name for Bay Hill Estates) and made Phase II subject to its Declaration. The apparent intent of this was to allow Phase II to have a separate sub-association for the governance of its limited common elements. Later in September 1988 the owner of Phase II declared Phase II was annexed to Estates Holdings, P.U.D.

In August 2005 a 100 acre property known as the LYEC III/Campbell property was annexed into the Association. There are 34 platted one acre lots comprising Plat 3 of Phase I, Bay Hill Estates. The assessments for these 34 lots were not paid as originally required. Legal proceedings in 2008 resulted in an agreement that the assessments up to the date of the agreement remained due, but future assessments and other charges would accrue until the lots were sold. The Campbell lots are located in the southwest corner of the property; the area is undeveloped.

This golf course property is not owned by the Association. The 146 acre golf course facility has an Association membership right and obligation for an equivalent 6.5 homes. The history is it started as the Stonewal Country Club and was incorporated in February 1984. The golf course went bankrupt and was acquired by PGA National Golf and Sports. The course is known as the Estate course and is operated independently from the Association. As a courtesy, PGA National offers residents of Bay Hill Estates the same paid membership privileges as PGA National residents.

Phase II encompasses approximately 485 acres of land, including developable land and preserve areas. It was purchased out of bankruptcy by Lennar/Centrex. Lennar named the property the Preserve at Bay Hill Estates, platted the property and started construction of model homes. Lennar recorded its Declaration in May 2008 in Palm Beach County Public Records Book 22669 Page 1594. Lennar/Centrex declared bankruptcy and CRVI (Cypress Realty) acquired the property in August 2008 and in October 2011 agreed to sell lots to Palm Beach West Associates III (PBWA), a subsidiary of GL Homes. PBWA initiated building and selling of homes and subsequently entered an agreement to purchase all 196 lots. The Preserve has a separate Home Owners Association for their limited common property. An agreement was reached in 2015 between Bay Hill Estates (Phase I) and the Preserve at Bay Hill Estates (Phase II) clarifying the relationship of the two communities. The agreement is recorded in the public records of Palm Beach County in book 27211 page 1772. It essentially makes the two communities independent of each other, provides use easement rights, confirms that the general common elements of Phase I are managed exclusively by Phase I, obligates Phase II to proportionally support the general common elements expenses as established by Phase I and subjects Phase II to the Rules and Regulations.