Water masers have been observed in several high-redshift active galactic nuclei, including the gravitationally lensed quasar MG 0414+0534. This quasar is lensed into four images, and the water maser is detected in two of them. The broadening of the maser emission line and its velocity offset are consistent with a group of masers associated with a quasar jet. If the maser group is microlensed we can probe its structure and size by observing its microlensing behaviour over time. We present results of a high-resolution numerical analysis of microlensing of the maser in MG 0414+0534, using several physically motivated maser models covering a range of sizes and emission profiles. Time-varying spectra of the microlensed maser are generated, displayed and analysed, and the behaviour of the different models compared. The observed maser line in MG 0414+0534 is consistent with maser spots as in other quasar jets, provided substructure is de-magnified or currently lost in noise; otherwise smooth extended maser models are also candidates to generate the observed spectrum. Using measures of spectral variability we find that if the maser has small substructure of ∼0.002 pc then a variation of 0.12 mag in flux and 2.0 km s−1 in velocity centroid of the maser line could be observed within two decades. For the smallest maser model in this study a magnification of >35 is possible 22 per cent of the time, which is of significance in the search for other lensed masers.