We measured water quality monthly for 22 years in water entering, within, and exiting a 65 km(2) shallow polymictic and eutrophic freshwater lake in the northern Gulf of Mexico. Fertilizer use in the watershed is the dominate source of phosphorous (P) going into the lake and controls the lake's P concentrations, but nitrogen (N) fertilizer use was not related to total nitrogen concentration in the lake. Half of the particulate P entering the lake is trapped within it and there is a net accumulation of N that appears to be from the stimulation of nitrogen fixation. The lake's concentration of Chlorophyll a (mu g Chl a l(-1)) and increase in N in the lake was directly related to the concentration of P in water entering the lake. Variations in the Chl a concentration within a freshwater lake downstream are also directly related to the annual use of P fertilizer, but not to N fertilizer use. Reducing agriculture-sourced P runoff will lower (but not eliminate) both the frequency of algal blooms within Lac des Allemands and the amount of N delivered to the estuary.