Coeur d'Alene Lake in northern Idaho is fed by two major rivers: the Coeur d'Alene River from the east and the St. Joe River from the south, with the Spokane River as its outlet to the north. This phosphorus-limited lake has been subjected to decades of mining (primarily for zinc and silver) and other anthropogenic inputs. A 32 full-factorial experimental design was used to examine the interactive effects of free (uncomplexed) zinc ion and dissolved-orthophosphate concentrations on phytoplankton that were isolated from two sites along a longitudinal zinc-concentration gradient in Coeur d'Alene Lake. The two sites displayed different dominant taxa. Chlorella minutissima, a dominant species near the southern St. Joe River inlet, exhibited greater sensitivity to free Zn ions than Asterionella formosa, collected nearer the Coeur d'Alene River mouth with elevated dissolved-zinc concentrations. Empirical phytoplankton-response models were generated to describe phytoplankton growth in response to remediation strategies in the surrounding watershed. If dissolved Zn can be reduced in the water column from >500 nM (i.e., current concentrations near and down stream of the Coeur d'Alene River plume) to <3 nM (i.e., concentrations near the southern St. Joe River inlet) such that the lake is truly phosphorus limited, management of phosphorus inputs by surrounding communities will ultimately determine the limnologic state of the lake.