Wular Lake, one of Asia’s largest freshwater lakes and a designated Ramsar site, supports vital fisheries that sustain thousands of local households. Despite its ecological and socio-economic importance, the lake has undergone rapid degradation due to siltation, pollution, encroachment, and invasive species expansion. The present study investigates the ichthyofaunal composition, biodiversity patterns, and catch per unit effort (CPUE) in Wular Lake over one annual cycle using data derived from field observations and fisher-based sampling across five sites—Lankreshpora, Laharwalpora, Ashtangoo, Watlab, and Sopore Ghat—to establish an updated baseline for biodiversity assessment. A total of eleven fish species, belonging to one order (Cypriniformes), two families (Cyprinidae and Balitoridae), and nine genera, were recorded, namely, Cyprinus carpio var. communis, Cyprinus carpio var. specularis, Carassius carassius, Schizopyge niger, Schizothorax esocinus, Schizothorax plagisotomus, Schizothorax labiatus, Schizothorax curvifrons, Crossocheilus diplocheilus, Triplophysa marmorata, and the critically endangered Triplophysa kashmirensis. The presence of T. kashmirensis highlights the ecological significance of Wular Lake as a refuge for threatened Himalayan fish species. These findings highlight the need for strengthened conservation actions and continuous monitoring to safeguard the lake’s diminishing native ichthyofaunal resources. Diversity indices were low to moderate and differed significantly among sites (Shannon–Wiener H′: F = 3.12, p = 0.022), with clear signs of declining native Schizothorax populations. Catch per unit effort (CPUE) differed significantly among sites (one-way ANOVA: F = 8.35, p < 0.001), being highest at Lankreshpora (868.75 g/man-hour) and lowest at Laharwalpora (99.60 g/man-hour), whereas catch did not vary significantly among seasons (F = 0.256, p = 0.855). The exotic common carp (Cyprinus carpio var. communis) was the single most dominant species, accounting for ~41% of the total biomass. These findings provide a baseline for the management interventions required for restoring the fishery of this critical Himalayan wetland.