Seagrass beds provide critical nursery habitats and spawning grounds for new generations of fish. The habitats are under threat from human activities and climate change, and with that, an important ocean service is lost that limits fish production. The present study investigates patterns in the larval occurrence and abundance in seagrass meadows at two locations with varying degrees of seagrass fragmentation. Monthly ichthyoplankton sampling was conducted during the northeast monsoon (NEM) and southeast monsoon (SEM) seasons in 2019 and 2020. A total of 42 larval fish families belonging to 37 genera and 21 species were identified. Dominant families were Labridae (29.5%), Blenniidae (28.7%), Gobiidae (26.0%), Engraulidae (23.3%) and Scaridae (22.3%). Canonical Correspondence Analysis and regression analysis revealed water temperature, dissolved oxygen and pH as the most important abiotic variables driving taxonomic composition of larval assemblages, while zooplankton and chlorophyll-a were the most important biotic factors. Fish larvae were more abundant in healthy seagrass habitats as compared to degraded ones. However, despite some loss in functionality, the degraded sites equally played a role in supporting some species, including Gobiidae and Blenniidae. Seasonality influenced larval abundance at the two sites, with a peak in mean abundance coinciding with the NEM season. Interannual variability in fish larval abundance was observed at both sites, indicating that factors controlling larval production varied between the years. This study demonstrates the important role of seagrass meadows in the replenishment of fish stocks and supportive evidence for their management and conservation.