This study assessed the vulnerability of 16 floodplain wetlands (beels) of the Lower Brahmaputra Valley, Assam, India, in relation to a range of natural and anthropogenic factors including climate change. The total water-spread area of the selected beels varied widely (8–50 ha), with 68.75% of the beels showing a reduction in water-spread area over the past 30 years. High levels of siltation and encroachment and detachment of marginal areas through the construction of roads were the major factors responsible for the reduction in the water-spread area of the beels. The reduction was observed to be in the range of over 33% in three beels (Raghunath Sora, Chulkani, and Dudua beel) to 83% in Bhoishpuri beel. In addition, one beel (Chulkani) experienced reduction in its deep pool area, which is an important wetland area that provides shelter to brood fishes during the dry season. Only 12.5% of the beels studied practiced enclosure (pen) culture for rearing fish. None practiced cage culture. Our study showed that only two beels (Bhoishpuri and Tariachora) were free from exotic fishes; the remaining surveyed beels reported exotic species such as, Cyprinus carpio (Common Carp), Ctenopharyngodon idella (Grass Carp), Hypophthalmichthys molitrix (Silver Carp), H. nobilis (Bighead Carp) and Piaractus brachypomus (Pacu). The prevalence of exotic fishes in the majority of the beels (due both to escape from nearby aquaculture ponds during floods and intentional stocking in certain beels) would have adversely affected the diversity of indigenous fishes in those wetlands. From discussion with the fishers, 50% of the beels surveyed experienced a reduction in the number of fish species from that recorded 10–20 years ago. In addition to climate change-related factors (e.g. abnormal rains, floods, or drought-like situations), other factors – both natural (e.g. hyper-nutrification) and anthropogenic (e.g. construction of roads, houses, and other structures) – also adversely affected the studied wetlands. To help cope with these factors and increase the adaptive capacity of fishers, four measures aimed at mitigation are suggested. These are: the practice of enclosure aquaculture in beels; the construction of floating macrophyte refuges (katal); deep pool refuges; and stock enhancement programmes with climate-resilient indigenous fishes.