In proton magnetic resonance spectroscopy (1H MRS) thermometry, separately acquired full water and partially suppressed water are commonly used for measuring temperature. This paper compares these two approaches. Single‐voxel 1H MRS data were collected on a 3‐T GE scanner from 26 human subjects. Every subject underwent five continuous MRS sessions, each separated by a 2‐min phase. Each MRS session lasted 13 min and consisted of two free induction decays (FIDs) without water suppression (with full water [FW or w]) and 64 FIDs with partial water suppression (with partially suppressed water [PW or w’]). Frequency differences between the two FWs, the first two PWs, the second FW and the first PW (FW2, PW1), or between averaged water (
wav′) and N‐acetylaspartate (NAA), were measured. Intrasubject and intersubject variations of the frequency differences were used as a metric for the error in temperature measurement. The intrasubject variations of frequency differences between FW2 and PW1
()fw2−fw1′, calculated from the five MRS sessions for each subject, were larger than those between the two FWs or between the first two PWs (p = 1.54 x 10−4 and p = 1.72 x 10−4, respectively). The mean values of intrasubject variations of
()fw2−fw1′ for all subjects were 4.7 and 4.5 times those of
()fw2−fw1 and
()fw2′−fw1′, respectively. The intrasubject variations of the temperatures based on frequency differences,
()fw2−fNAA or (
fw1′−fNAA), were about 2.5 times greater than those based on averaged water and NAA frequencies
true(fwitalicav′−fNAA). The mean temperature measured from
true(fwitalicav′−fNAA) (n = 26) was 0.29°C lower than that measured from
()fw2−fNAA and was 0.83°C higher than that from (
fw1′−fNAA). It was concluded that the use of separately acquired unsuppressed or partially suppressed water signals may result in large errors in frequency and, consequently, temperature measurement.