Many large lake ecosystems are experiencing increasing eutrophication and persistent cyanobacteria‐dominated algal blooms affecting their water quality and ecosystem productivity because of widespread non‐point and point nutrient sources. Accordingly, the present study utilized data of July 2003 and January–February 2004, as well as previous measurements of nutrients and physico‐chemical variables (electrical conductivity, dissolved oxygen, temperature, pH, turbidity and chlorophyll‐a), to characterize the spatial and temporal trends, as a means of better understanding the factors influencing lake environmental conditions, as support tools for long‐term ecosystem management and for better understanding the long‐term trends and effects. Inshore gulf areas were found to represent zones of maximum nutrient concentrations, compared to the deep main lake zones, with significant inter‐parameter correlations. Phosphorus, silicon and chlorophyll‐a concentrations were significantly correlated. Water electrical conductivity was also significantly and positively correlated with soluble reactive silicon (SRSi), alkalinity hardness DO, while exhibiting a negative association with water transparency. Water turbidity and transparency, electrical conductivity, and SRSi concentrations clearly describe a gradient from the gulf into the main lake. For such a shallow gulf, these findings suggest primary productivity is influenced mainly by the availability of nutrients, light transparency and the extent of availability of resuspended nutrients. The increasing eutrophic state of Lake Victoria is a serious concern since it contributes to an increased potential of more frequent occurrences of cyanobacterial blooms, a potential public health risk to both humans and wildlife. Improved understanding of influences from previous fish species introductions and concomitant changes in indigenous fish species, increased lake basin population and anthropogenic activities, water hyacinth resurgences, sustainability of biodiversity, and current interests in cage farming, are among the major concerns and challenges facing the contemporary Lake Victoria. The trends regarding nutrients and physico‐chemical characteristics are intended to support better monitoring efforts and data to promote the lake's ecosystem services and the sustainable management of the lake ecosystem.