Impacts of Cage Aquaculture on Benthic Biodiversity in Tropical Freshwater Ecosystems: A Case of Lake Victoria, Kenya

Cage aquaculture is expanding rapidly in Lake Victoria, Kenya, but its ecological consequences for benthic biodiversity remain insufficiently characterized. This study presents a comparative analysis of benthic macroinvertebrate communities in cage farming and non-farming areas across five representative sites: Dunga, Naya, Ndere, Sena, and Rasira. These were selected along a limnological gradient spanning sandy, muddy, and rocky substrates. Fieldwork was conducted in March 2023 and 2024, combining benthic sampling using Ekman grabs, water quality assessments with multi-parameter probes, and laboratory analyses of macroinvertebrate composition, diversity, and pollution tolerance. Data were evaluated through univariate and multivariate techniques, including negative binomial generalized linear models and principal component analysis. A total of 19 macroinvertebrate taxa were recorded, with species richness consistently lower at farming sites. Shannon-Weiner diversity indices confirmed reduced diversity at cage locations, while tolerant taxa such as Chironomus tentans and Melanoides tuberculata dominated farming areas. Hilsenhoff Biotic Index values indicated fair to severely impaired conditions at cage sites, reflecting considerable organic enrichment, whereas non-farming sites exhibited better ecological status. Multivariate ordination demonstrated distinct community clustering linked to farming status and pollution gradients. The findings provide robust evidence that cage aquaculture alters benthic community structure through localized organic enrichment, favoring opportunistic species at the expense of sensitive taxa. These insights emphasize the need for ecosystem-based management, incorporating benthic monitoring to mitigate localized degradation while sustaining fish production. The study delivers critical baseline data to guide sustainable aquaculture development and conservation planning in Lake Victoria and other large tropical lakes undergoing aquaculture intensification.