In the Matang Mangrove Forest Reserve (MMFR), the role of microzooplankton (20–200 μm) grazing on phytoplankton as a channel for carbon transfer to higher trophic levels was investigated. Our results showed that primary production was higher during the southwest monsoon (SWM) (1905 ± 1478 μgCl−1d−1) than in the northeast monsoon (NEM) (708 ± 474 μgCl−1d−1). Microzooplankton grazing was tightly coupled to primary production in both SWM and NEM, accounting for 97% and 68% of primary production, respectively. Both primary production (activation energy: 1.29 ± 0.54 eV) and microzooplankton grazing (2.05 ± 0.63 eV) showed temperature dependency, and revealed a shift towards heterotrophy with seawater warming, specifically at temperatures above 32 °C. As a conclusion, the microbial food web in MMFR is characterised by high primary production that was efficiently grazed by microzooplankton.