This study evaluates changes in fish species diversity over time in Hakaluki Haor, an ecologically critical wetland in Bangladesh, and the factors affecting this diversity. Fish species diversity data were collected from fishers using participatory rural appraisal tools and the change in the fish species diversity was determined using Shannon-Wiener, Margalef's Richness and Pielou's Evenness indices. Principal component analysis (PCA) was conducted with a dataset of 150 fishers survey to characterize the major factors responsible for the reduction of fish species diversity. Out of 63 fish species, 83% of them were under the available category in 2008 which decreased to 51% in 2018. Fish species diversity indices for all 12 taxonomic orders in 2008 declined remarkably in 2018. The first PCA (climatic change) responsible for the reduced fish species diversity explained 24.05% of the variance and consisted of erratic rainfall (positive correlation coefficient 0.680), heavy rainfall (−0.544), temperature fluctuation (0.561), and beel siltation (0.503). The second PCA was anthropogenic activity, including the use of harmful fishing gear (0.702), application of urea to harvest fish (0.673), drying beels annually (0.531), and overfishing (0.513). Finally, the third PCA was loaded with the fishermen age (0.719), education (−0.767), and fishing experience (0.695) of the fishers. Deepening of beels could enhance dry season water availability and shelter the fish. Imposing fisheries regulations to reduce human activities is inevitable to sustain haor fisheries.