Ecological models facilitate the evaluation and assessment of alternative approaches to restore the Greater Everglades ecosystem. Joint Ecosystem Modeling (JEM) provides ecological models tailored to address specific management issues. The multi-agency REstoration, COordination and VERification (RECOVER) science team uses ecological models (i.e., ecological planning tools) to evaluate the potential effects of projects in the Comprehensive Everglades Restoration Plan (CERP) on natural resources. The planning agencies and bureaus involved in CERP desire to also use these ecological planning tools for the evaluation of alternative water control plans to be performed by the Lake Okeechobee System Operating Manual (LOSOM) Project Delivery Team (PDT). The models of particular interest to the LOSOM PDT are: (1) Marl Prairie Habitat Suitability Index in conjunction with the (2) Cape Sable Seaside Sparrow Helper, (3) (native) Apple Snail population model (EverSnail), (4) Snail Kite Nesting Habitat Selection model (KiteNest) (5) Wading bird occupancy model (EverWaders), (6) Small-sized freshwater fish density, and (7) American alligator habitat suitability index (HSI). The LOSOM PDT evaluates water control plans using an iterative process to ultimately arrive at a final plan that balances flood control, water supply, navigation, recreation, and preservation of fish and wildlife resources. This data release provides ecological model outputs for iteration 1 and 2 (of 3). Ecological modeling outputs for LOSOM iteration 3 (of 3) can be found at the following location: https://doi.org/10.5066/P9NOM50H.