The floodplain wetlands in different regional settings vary with time and space in terms of function and geomorphological diversity. In recent decades, these eco-sensitive waterbodies have been exposed to a wide range of anthropogenic threats and climatic changes. Therefore, assessment of these ecological and environmental threats is prerequisite to understand the state of ecosystem and to develop a sustainable management strategy for conservation of wetland biodiversity and fisheries enhancement. This paper discusses the region-specific pattern of trophic state index (TSI) of the 27 floodplain wetlands in West Bengal, India. Carlson TSI and Lamparelli TSI methods were used to determine a better approach based on historical and continuous dataset and to delineate the interrelationship among historical climatic variability for sustainable management of the resources. The study revealed that agro-climatic divisions do not unveil any significant impact on the TSI calculated using Carlson TSI as well as Lamparelli TSI method. The TSI scores for the two methods were significantly different (p < 0.01) for different zones based on wetland habitat types. The TSI scores revealed most of the wetlands to be in mesotrophic state. Principal component analysis (PCA) indicated that TSI scores were having similar pattern of variation with rainfall and water temperature. The present study also conveys fundamental information on ecological status based on the trophic state, which will aid to develop region-specific strategies for sustainable fisheries enhancement.