Population-based habitat conservation planning for migrating and wintering waterfowl in North America is carried out by habitat Joint Venture (JV) initiatives and is based on the premise that food can limit demography (i.e. food limitation hypothesis). Consequently, planners use bioenergetic models to estimate food (energy) availability and population-level energy demands at appropriate spatial and temporal scales, and translate these values into regional habitat objectives. While simple in principle, there are both empirical and theoretical challenges associated with calculating energy supply and demand including: 1) estimating food availability, 2) estimating the energy content of specific foods, 3) extrapolating site-specific estimates of food availability to landscapes for focal species, 4) applicability of estimates from a single species to other species, 5) estimating resting metabolic rate, 6) estimating cost of daily behaviours, and 7) estimating costs of thermoregulation or tissue synthesis. Most models being used are daily ration models (DRMs) whose set of simplifying assumptions are well established and whose use is widely accepted and feasible given the empirical data available to populate such models. However, DRMs do not link habitat objectives to metrics of ultimate ecological importance such as individual body condition or survival, and largely only consider food-producing habitats. Agent-based models (ABMs) provide a possible alternative for creating more biologically realistic models under some conditions; however, ABMs require different types of empirical inputs, many of which have yet to be estimated for key North American waterfowl. Decisions about how JVs can best proceed with habitat conservation would benefit from the use of sensitivity analyses that could identify the empirical and theoretical uncertainties that have the greatest influence on efforts to estimate habitat carrying capacity. Development of ABMs at restricted, yet biologically relevant spatial scales, followed by comparisons of their outputs to those generated from more simplistic, deterministic models can provide a means of assessing degrees of dissimilarity in how alternative models describe desired landscape conditions for migrating and wintering waterfowl.