Study aimed at evaluating phytoplankton biodiversity changes in a shallow tropical reservoir during its hypertrophication process. Samplings were carried out monthly during 8 consecutive years (1997-2004) in 5 depths. Conspicuous limnological changes in the reservoir derived from the presence and/or removal of the water hyacinth, characterized 3 different phases. Over the time series, reservoir changed from a typical polymictic eutrophic system to hypertrophic one, leading to a reduction of approximately 70 species (average 37%). Chlorophyceae accounted for the highest species richness (46%) among all algal classes and strictly followed total species richness variation. Internal feedback mechanisms intensification over phase III clearly promoted the sharp decrease in biodiversity. Highest decreases, mainly during springs, occurred simultaneously to the highest Cyanobacteria blooms. Increased turbidity due to heavy phytoplankton blooms suppressed all other algal groups, so that at the end of the present study even Cyanobacteria species richness decreased. Total dissolved phosphorous was included in most of the best selected models used to analyze the temporal patterns in species richness loss. Present data show that biodiversity loss following trophic change was not a single dimension of a single factor but, rather, a template of factors (e.g. light, stability) co-varying in consequence of the larger levels of biomass supported in the reservoir.