AbstractThe effects of potential reductions of freshwater inflow were evaluated for the lower Peace River and its largest tributary, lower Shell Creek, which flow into the Charlotte Harbor estuary in southwest Florida. Habitat suitability modeling (HSM) and mapping of fish and invertebrate species life stages were used to seasonally predict changes in spatial distributions and population numbers associated with simulated freshwater withdrawals. Seasonal salinity grids and temperature grids derived from values predicted by hydrodynamic modeling (2007–2014) were similar between baseline (i.e., flows not affected by water withdrawals) and minimum flows (flows associated with water withdrawals). Depth grids, bottom type grids, and seasonal dissolved oxygen grids were held constant between the two scenarios. Seasonal habitat suitability models were applied to 28 fish and invertebrate species life stages with affinities for low or moderate salinity. Salinity was the most significant factor in seasonal models for species life stages. The seasonal HSM maps produced showed that spatial distributions were similar between baseline and minimum flows for each species life stage. Most seasonal estimates of population numbers under minimum flows were less than the estimates for the baseline condition, indicating some effect on population numbers associated with flow reductions. Reductions in population numbers under minimum flows ranged from 0.3% to 21.0%, with 3 out of 28 seasonal comparisons indicating losses >15% and 12 comparisons indicating losses between 5% and 15%. Although other factors related to freshwater inflow can also influence species abundance and distribution, these results demonstrate how output from hydrodynamic modeling can be applied to HSM analyses and mapping to estimate spatial changes in habitat areas and population numbers for the life stages of selected fish and invertebrate species in relation to changes in salinity distributions, which can be used to identify areas of an estuary that are particularly susceptible to the effects of inflow reductions.