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I estimate changes in agricultural land value discounts due to prairie pothole habitat. The implicit prices of pothole habitat acreage are estimated from a series of hedonic models using Manitoba agricultural land transaction data from 1990 to 2009. I find that the discount on wetland acreage increased by at least 40%, suggesting that significant unanticipated increases in the benefits of converting wetlands emerged over the course of the study period. I also estimate a series of quantile regression hedonic models. The quantile regression models indicate that the land value discounts on prairie pothole acreage as a percent of per acre sales prices are constant across the land value distribution. These results have implications for the design of habitat conservation programs, particularly those involving long‐term agreements between landowners and conservation agencies.