Ecological models facilitate evaluation and assessment of alternative approaches to restore the Greater Everglades ecosystem. However, the provision of useful and accessible models is a challenge because there is often a disconnect between model output and its use by decision makers. Joint Ecosystem Modeling (JEM) meets this challenge by providing ecological model output tailored to management decisions. JEM is a partnership among Federal and state agencies, universities, and other organizations. Ecological models (i.e., ecological planning tools) were used by the multi-agency REstoration, COordination and VERification (RECOVER) science team during the Central Everglades Planning Project (CEPP) and Interim Goals Interim Targets (IGIT) planning to evaluate potential effects to natural resources within the study area. RECOVER is required to perform a system-wide evaluation of the Comprehensive Everglades Restoration Plan (CERP) and IGIT per the 2003 programmatic regulations. The purpose of IGIT is to predict the performance of specific ecological indicators as they relate to the implementation of CERP to ensure that the goals and objectives of the project are being met. The models used were: (1) Cape Sable Seaside Sparrow Marl Prairie Indicator in conjunction with (2) Cape Sable Seaside Sparrow Helper, (3) Florida apple snail (native) population model (EverSnail), (4) Wader Distribution Evaluation Modeling (WADEM), (5) Small-sized freshwater fish density, and (6) American alligator production probability (i.e., habitat suitability index (HSI)). These ecological models are used to examine potential impacts on the above listed flora and fauna in evaluation of the update of the IGIT Technical Report.