The sixteenth-century church, Iglesia San José, in San Juan, Puerto Rico, was placed on the World Monuments Watch List in 2004. Originally known as the Iglesia de Santo Tomás de Aquino, it is considered by many scholars to be one of the finest and oldest examples of Gothic-influenced religious architecture built by the Spanish in the New World. Water infiltration and structural issues were at the core of the closing of the structure in 2002 after which emergency conservation measures were developed together with a long-term restoration plan. Both the development of the restoration plan and the conservation measures were enhanced by the use of ground-penetrating radar with both midrange and high-frequency antennas. Subsurface water infiltration and subsequent voids were effectively mapped to help determine patterns of rainwater travel through the stone and rubble masonry walls. Ground-penetrating radar results also provided evidence of multiple construction phases and modifications and corroborated or enhanced architectural evidence used to understand the construction sequences.