Seasonal cycles, interannual variations and decadal trends of Sea-viewing Wide Field-of-view Sensor (SeaWiFS)-retrieved chlorophyll-a concentration (Chl-a) in the Strait of Malacca (SM) were investigated with reconstructed, cloud-free SeaWiFS Chl-a during the period of the SeaWiFS full mission (September 1997 to December 2010). Pixel-based non-parametric correlations of SeaWiFS Chl-a on environmental variables were used to identify the probable causes of the observed spatio-temporal variations of SeaWiFS Chl-a in northern, middle and southern regions of the SM. Chl-a was high (low) during the northeast (southwest) monsoon. The principal causes of the seasonality were wind-driven vertical mixing in the northern region and wind-driven coastal upwelling and possibly river discharges in the middle region. Among the three regions, the southern region showed the largest interannual variations of Chl-a. These variations were associated with the El Niño/Southern Oscillation (ENSO) and river runoff. Interannual variations of Chl-a in the middle and northern regions were more responsive to the Indian Ocean Dipole and ENSO, respectively, with atmospheric deposition being the most important driver. The most significant decadal-scale trend of increasing Chl-a was in the southern region; the trend was moderate in the middle region. This increasing trend was probably caused by environmental changes unrelated to the variables investigated in this study.