2005 photo at the first mission site (#1) by David Kier.
GPS: 31°34'11.0" 116°28'50.0" The Santo Tomas mission was first located some 2 1/2 miles west of the town of Santo Tomas. Two sets of ruins (1 mile apart) have been photographed and both called the first mission location (site #1 and site #2):
Peveril Meigs, in 1926 only documented site #2 and site #3. Meigs called site #2 the 'first site'. Peter Gerhard (in 1956) and Michael Mathes (in 1977) do not mention site #2, only site #1 as the first site and a move in 1794 to site #3.
Zephyrin Engelhardt (1929) gives the year 1794 for a move "higher up" (p 575). Engelhardt (p 625) then provides the founding date of April 24, 1791, the first move in June, 1794, and a second move "on account of the lack of pastures" that was requested "8 years since the founding" (1799).
Site #1 is on the south side of the oak tree lined stream, on the valley floor. It should be considered the first location because mosquitos and flooding were reasons for a move "higher up", made in 1794. The mountain blocking direct sunlight was also a concern, wrote one padre.
The move from site #2 (because of the "lack of pastures") to the final site (#3) was made in 1799. Many adobe buildings were constructed there, yet almost nothing remains.
1977 photoghraph by Michael Mathes at the first site for
Santo Tomas mission. 
1949 photo at site #2 by Marquis McDonald. A photograph by
Peveril Meigs some 25 years earlier shows nearly the same. 
2005 photo at site #3 by David Kier. Located just north of
the 'El Palomar' campground, on the east side of Hwy. 1. GPS: 31°33'30.0"
116°24'48.9" 
1926 photo at site #3 by G.W. Hendry 
1949 photo at site #3 by Marquis McDonald 
1975 photo at site #3 by Robert Jackson