A Habitat Suitability Index (HSI) model was developed using four environmental variables (bottom temperature, bottom salinity, depth, and bottom substrate type) and 29 years of spring and fall lobster surveys for evaluating the spatiotemporal variability of suitable lobster habitat in Long Island Sound (LIS). The suitability indices calculated for the four environmental variables were combined to form a composite HSI using an arithmetic mean model and geometric mean model. A cross-validation study was conducted to evaluate the predictive performance of the HSI models. Annual geographic information system maps of estimated HSI values were produced using Kriging interpolation for adult and juveniles in spring and fall from 1978 to 2012. The overall spatial distribution of suitable habitat for lobster was mainly concentrated in the western-central part of LIS during spring (April–June), but showed clustering patterns throughout LIS during fall (September–October). An examination of the temporal change in annual median HSI values identified possible time blocks when habitat conditions were extremely poor and revealed a statistically significant decreasing trend in availability of suitable habitat for juveniles during spring from 1978 to 2012. Spatiotemporal variability in availability of suitable habitat may imply changes in carrying capacity of LIS for the American lobster.