Plankton and macroinvertebrates are used as biodiversity indicators on account of their sensitivity to changes in aquatic ecosystems. This chapter assesses the changes in the diversity, abundance and distribution of plankton and macroinvertebrates in the inshore and offshore areas of Lake Victoria, selected satellite lakes and rivers within the lake basin. Samples for both plankton and macroinvertebrates were collected during dry and wet seasons between 2000 and 2006. The results indicated that cyanobacteria were most diverse in both seasons. Microcystis spp., Planktolyngbya spp. and Anabaena spp. were the most dominant cyanophyte species at the sampled sites. The dominant phytoplankton (cyanobacteria) are less digestible and provide poor quality food for the fish; that may have contributed to the reduction or loss of planktivorous haplochromines and tilapiines that once flourished in Lake Victoria. Zooplankton community composition in the lake is dominated by rotifers and cyclopoid copepods, in both inshore and offshore areas. The dominance of cyclopoid copepods is important in the production and sustainability of small fishes and larvae that utilize these organisms as a food base. Macroinvertebrate abundance has shifted from an oligochaete and insect dominated community in 1984 to a community dominated by molluscs. The occurrence of a relatively high abundance of low-oxygen tolerant macroinvertebrate taxa at inshore and offshore stations is an indication of deteriorating water quality water quality conditions due to eutrophication and pollution processes. There is a need for a reduction in nutrient loads and pollutant inputs into the lake in order to ensure the ecosystem health.World Bank (GEF/IDA) through LVEMP I