With increasing attention on the contribution of ecosystems to human well-being, there is a need for tools that integrate ecological and economic models for valuing ecosystem services. To address this, we develop a protocol for linking ecological processes and outcomes to human preferences, which combines environmental modeling, expert elicitation, and nonmarket valuation methods. Our application values reductions in nutrient loads to lakes in the southeastern US. The innovation centers on how biochemical measures of water quality (e.g., chlorophyll a) are translated into terms that are meaningful to individuals who derive ecosystem services from them. Using expert elicitation data, we estimate a model linking changes in biochemical measures to an index of eutrophication in lakes. We then develop a stated preference survey including (a) detailed descriptions of the perceptible outcomes – e.g., water color, clarity – associated each eutrophication index level; and (b) policy scenarios involving state-level changes in lake eutrophication conditions. We estimate a function that predicts households' willingness to pay for changes in lake water quality. We demonstrate the protocol through a case study examining the benefits of lake quality improvement in Virginia as a result of recent policies to reduce nutrient loads in the Chesapeake Bay watershed.