Amphibians are known to be sensitive to environmental change but their responses at the level of metacommunities to short-term environmental variability are poorly understood. We used field data from two protected areas, La Pera and Nahá (Chiapas, Mexico) to test for variation in metacommunity properties for two consecutive years (2009 and 2010). Amphibians and accompanying environmental data were recorded to a standardized protocol within each landscape, in four or five transects of 50 × 2-m per patch, for 30 and 31 patches, respectively. We found 23 species in La Pera and 30 in Nahá (21 species shared). Metacommunity structure was analysed using reciprocal averaging (RA) ordination by means of metrics for coherence, turnover and boundary clumping, with Spearman rank correlation used to examine relationships with environmental variables. The metacommunity structure varied differentially among the landscapes between years, being classed as quasi-Gleasonian in La Pera in both years, but Clementsian for Nahá in 2009 and Gleasonian for Nahá in 2010. In further illustration of variation between years, in 2009 the principal community gradient (RA axis 1) for La Pera was significantly positively correlated with altitude (r = 0.36), forest disturbance status (r = 0.78), mean canopy cover (r = 0.79) and mean litter depth (r = 0.67), while in 2010 it was correlated with latitude (r = 0.38), mean grass-layer height (r = 0.38), incidence of rainfall prior to sampling (r = 0.35) and presence of temporary ponds (r = 0.45). Our findings support the notion that amphibians respond to short-term environmental changes by individualistic movement within the landscape as well as via population dynamic responses.