The pigment content in leaves has commonly been used to characterize vegetation condition. However, few studies have assessed temporal changes of local biotic and abiotic factors on leaf pigments. Here, we evaluated the effect of local environmental variables and tree structural characteristics, in the chlorophyll-a leaf concentration (Chl-a) associated with temporal change in two mangrove species. Rhizophora mangle (R. mangle) and Avicennia germinans (A. germinans) trees of a fringe mangrove forest (FMF) and lower basin mangrove forest (BMF) were visited over a period of one year, to obtain radiometric readings at leaf level to estimate Chl-a. Measurements on tree characteristics included diameter at breast height (DBH), basal area (BA), and maximum height (H). Environmental variables included soil interstitial water temperature (Ti), salinity (Si), and dissolved oxygen (Oi), flood level (fL), ambient temperature (Tamb), and relative humidity (Hrel). Generalized linear models and covariance analysis showed that the variation of Chl-a is mainly influenced by the species, the interaction between species and mangrove forest type, DBH, seasonality and its influence on the species, soil conditions, and fL. Studies to assess spatial and temporal change on mangrove forests using the spectral characteristics of the trees should also consider the temporal variation of leave chlorophyll-a concentration.