Birds have been monitored as indicators of ecosystem health in both the freshwater and marine habitats of south Florida, USA for decades. This study reports on nine years (2010-2018) of monthly systematic surveys of breeding waterbird colonies in Biscayne National Park. Overall, 89% of active nests in the park belonged to Double-crested Cormorants (Phalacrocorax auritus). The annual sum of nest counts within the study area grew by 58% over the course of the study. This growth in the nesting population is driven by a 61% growth in northern colonies. During this same time period, the southern colonies declined to less than half their original size. These opposing trends coincide with differences in habitat quality (salinity, chlorophyll, sea grass density, and/or prey abundance) between the two regions. In addition, Hurricane Irma strongly impacted the nesting Double-crested Cormorants, suggesting a loss of nearly 400 nests, although four months post-storm nesting was back to normal levels. Finally, two colonies appear to have started during the study period in close proximity to recently completed Biscayne Bay Coastal Wetlands restoration projects. One of these colonies supported a maximum of over 350 nests.