Summary Collision of birds and bats with turbines in utility‐scale wind farms is an increasing cause of concern. Carcass counts conducted to quantify the ‘take’ of protected species need to be corrected for carcass persistence probability (removal by scavengers and decay) and detection probability (searcher efficiency). These probabilities may vary with time since death, because of intrinsic changes in carcass properties with age and of heterogeneity (preferential removal of easy‐to‐detect carcasses). In this article, we describe the use of superpopulation capture–recapture models to perform the required corrections to the raw count data. We review how to make such models age specific and how to combine trial experiments with carcass searches in order to accommodate the fact that carcasses are stationary (which affects the detection process). We derive information about optimal sampling design (proportion of the turbines to sample, number of sampling occasions, interval between sampling occasions) and use simulations to illustrate the expected precision of mortality estimates. We analyse data from a small wind farm in New Jersey, in which we find the estimated number of fatalities to be twice the number of carcasses found. Synthesis and applications. Our approach to estimation of wind farm mortality based on data from carcass surveys is flexible and can accommodate a range of different sampling designs and biological hypotheses. Resulting mortality estimates can be used (1) to quantify the required amount of compensation actions, (2) to inform mortality projections for proposed wind development sites and (3) to inform decisions about management of existing wind farms.