Lake Malawi National Park (LMNP) was created in 1980 to safeguard the rich freshwater fish biodiversity in Lake Malawi. However, the park is increasingly affected by anthropogenic activities in the surrounding upland areas and by encroachment, which threaten its ecological integrity. Despite this, limited information exists on temporal changes in fish abundance, species richness, diversity and assemblage structure across multiple islands and depth gradients within the park. This study assessed variations in fish populations at Mumbo, Domwe and Thumbi West Islands using surveys conducted in 2021 and 2025. At each site, transects were established parallel to the shoreline at depths of 3, 12 and 20 m. Along each transect, 2 × 2 m quadrats were placed at predetermined intervals, and all the fish observed within each quadrat were identified, counted and recorded. Differences in species richness and diversity across years, sites and depths were analysed using three-factor analysis of variance (ANOVA). A negative binomial generalized linear model (GLM) was used to evaluate the effects of year, site and depth on species abundance. Multivariate analyses examined variations in the fish assemblages and dominant species. Fish counts declined significantly by 47% between 2021 and 2025 (p < 0.001); however, species richness or diversity remained stable. Likewise, fish abundance was significantly lower at Mumbo, whereas species richness remained relatively stable across sites but declined significantly with increasing depth. The fish assemblages differed significantly across years, sites and depths. A total of 134 species were recorded, the majority being cichlids, with 93 species classified as Least Concern and 13 requiring conservation attention. These findings highlight the importance of LMNP as a critical conservation refuge for Lake Malawi; however, the decline in fish abundance warrants further investigation into potential drivers and calls for continued monitoring and adaptive management. Lake Malawi National Park management is to institute a fisheries resource monitoring program for the islands within the park.Comparable management measures are to be used in the management and conservation of the Lake Malawi National Park's islands.Lake Malawi National Park should consider providing streamlined regulatory and conservation frameworks for fish species that are vulnerable, endangered and critically endangered. Lake Malawi National Park management is to institute a fisheries resource monitoring program for the islands within the park. Comparable management measures are to be used in the management and conservation of the Lake Malawi National Park's islands. Lake Malawi National Park should consider providing streamlined regulatory and conservation frameworks for fish species that are vulnerable, endangered and critically endangered.