In response to declines in coarse woody habitat (CWH) and fish productivity in natural lakes and reservoirs, agencies and stakeholders have used woody and artificial habitat enhancements to slow or reverse the effects of habitat loss from aging or shoreline development. Given that natural lakes and reservoirs differ in physical and biological conditions that could influence habitat enhancement outcomes, a framework is needed to guide management expectations for CWH replacement under different ecosystem contexts. We review ecosystem contexts that influence the effects of structural habitat enhancements in natural lakes and reservoirs, use preliminary results from case studies in a natural lake in Wisconsin and two reservoirs in Illinois to illustrate the importance of these contexts, and provide management recommendations for habitat deployments that consider physical and biological ecosystem characteristics. Because of their influence on trophic transfer efficiency, trophic status and turbidity are important contexts for habitat enhancements in natural lakes and reservoirs. Habitat enhancements to large reservoirs must also contend with high nutrient loading, water level fluctuations, and longitudinal gradients in physical and biological conditions. Preliminary results from the Wisconsin experiment illustrated the importance of the recipient fish community, with rates of response to the structural enhancement varying among fish species. The Illinois case studies demonstrated how the magnitude of change (i.e., effect size) after habitat enhancement can differ (1) between CWH additions to an oligotrophic natural lake and a eutrophic, turbid reservoir and (2) by longitudinal position of artificial habitat within a large reservoir. The functions or ecosystem services of CWH targeted for rehabilitation provide guidance as to which ecosystem features will shape the strength, direction, and duration of response. Future whole-ecosystem manipulations are needed across a wider range of environmental contexts and fish productivity responses, and the strength of productivity increases should be compared to increased harvest efficiency.