Monthly time series, from 2001 to 2016, of the Normalized Difference Vegetation Index (NDVI) and the Enhanced Vegetation Index (EVI) from MOD13Q1 products were analyzed with Seasonal Trend Analysis (STA), assessing seasonal and long-term changes in the mangrove canopy of the Teacapan-Agua Brava lagoon system, the largest mangrove ecosystem in the Mexican Pacific coast. Profiles from both vegetation indices described similar phenological trends, but the EVI was more sensitive in detecting intra-annual changes. We identified a seasonal cycle dominated by Laguncularia racemosa and Rhizophora mangle mixed patches, with the more closed canopy occurring in the early autumn, and the maximum opening in the dry season. Mangrove patches dominated by Avicennia germinans displayed seasonal peaks in the winter. Curves fitted for the seasonal vegetation indices were better correlated with accumulated precipitation and solar radiation among the assessed climate variables (Pearson’s correlation coefficients, estimated for most of the variables, were r ≥ 0.58 p < 0.0001), driving seasonality for tidal basins with mangroves dominated by L. racemosa and R. mangle. For tidal basins dominated by A. germinans, the maximum and minimum temperatures and monthly precipitation fit better seasonally with the vegetation indices (r ≥ 0.58, p < 0.0001). Significant mangrove canopy reductions were identified in all the analyzed tidal basins (z values for the Mann-Kendall test ≤ −1.96), but positive change trends were recorded in four of the basins, while most of the mangrove canopy (approximately 87%) displayed only seasonal canopy changes or canopy recovery (z > −1.96). The most resilient mangrove forests were distributed in tidal basins dominated by L. racemosa and R. mangle (Mann-Kendal Tau t ≥ 0.4, p ≤ 0.03), while basins dominated by A. germinans showed the most evidence of disturbance.