Defining water quality seascapes in the KJCAP, their relationship to hydrographic modeling connectivity, the 2023 coral bleaching, and SCTLD

Reduced water quality on Florida’s Coral Reef (FCR) from anthropogenic sources has long been implicated in the decline of the reef system. Florida’s Coral Reef is experiencing significant coral declines due to thermal stress and disease, which is exacerbated by environmental factors such as nutrient pollution. This study identified hydrographic connections between inland water sources in southeast Florida (Government Cut, Baker’s Haulover, Port Everglades, and Hillsboro) and coral reefs and investigated the environmental drivers associated with bleaching and disease between 2018 and 2024. 

Our machine-learning models explained 41.5 – 78.9% of the variation in the water quality concentrations on the reef with many contributing factors in various analytes including inlet outflow, rainfall, and high winds, however year had a high influence in almost every test. In almost every case, while holding all other predictors at their mean, the model showed nutrient increasing over time. Orthophosphate showed a lower annual increase after 2021, supporting that the Miami-Dade county fertilizer restrictions may be helping to reduce the rate of annual increase. 

Hydrographic models showed that the reefs northward of their adjacent inlet are most exposed to the water from that inlet and from inlets further south, but there is also a seasonal non-negligible southern footprint extending tens of kilometers. Government Cut and Baker’s Haulover discharge the largest nutrient loads and reducing pollutant loads in the Biscayne Bay system would significantly reduce excess nutrients in the KJCAP. 

The machine-learning models explained 93% of the variation of partial bleaching of 5% or greater mostly driven by colony, landward winds, and temperature, which supports that some colonies are more sensitive than others and turbidity from high winds may help reduce bleaching. The SCTLD models explained 46% of the variation in lesions driven by colony, modeled silicate, and hot snaps, supporting some colonies are more disease resistant and that increased exposure to terrestrial waters increases SCTLD lesions. 

The highest SCTLD prevalence in five years on the monitored O. faveolata colonies was recorded in July 2023. In August, the colonies south of Government Cut had the highest recorded bleaching, which took about five months to recover (no mortality from bleaching was observed), whereas no colonies further north visibly bleached. Unbleached colonies continued to acquire SCTLD lesions in the north, whilst SCLTD quiesced on bleached colonies. Thus, it appears that high temperatures in early and mid-summer exacerbated SCTLD, but the higher temperatures south of Government Cut caused those corals to bleach, which quiesced SCTLD in those colonies.

Government Cut has been identified as a major transition between ecoregions in SE FL where significant Thalassia seagrass beds exist in the oceanside nearshore habitats further south (Biscayne ecoregion), but none further north. Seasonal analysis of the water quality sites indicated that the waters in the Biscayne ecoregion were distinctly different most of the time over five years on average having lower nitrate, nitrite, and TSS and higher silicate and orthophosphate. Sea grasses uptake large amounts of nutrients for seagrass growth and 3 PO C3D88F June 2025 can cause imbalances in their ratios, which can be exacerbated in warmer temperatures. Since the ratios of C: N: P: Fe determines the effect of nutrients on coral health, it is possible that the ocean side seagrass beds in Biscayne are affecting the water chemistry and increasing the corals susceptibility to thermal stress and bleaching. In 2023, nearshore reef temperatures south of Government Cut were warmer than further north, however there were also regional differences in nutrient concentrations. The water quality monitoring sites between Government Cut and Baker’s Haulover had much higher total phosphorus, nitrate, silicate, and nitrite than those south of Government Cut. A lack of phosphorus can inhibit Symbiodiniaceae cell division and metabolism weakening the corals resistance to stress. In the 2023 wet season, the average values of total phosphorus in Biscayne were 4.7 times lower than normal and nitrate was 1.6 times lower. 

This study provides crucial insights into the hydrographic dynamics affecting coral reefs in Southeast Florida. By identifying key nutrient sources and their relationship to bleaching and disease, it lays the groundwork for effective management actions to mitigate coral disease and promote reef resilience. These findings highlight the importance of managing inland water quality to protect coral reefs. The model provides a detailed understanding of how nutrients from inland sources are transported to reefs, offering valuable insights for targeted intervention strategies. We recommend extending the model’s spatial footprint to capture the hydrodynamics of the entire FCR in the same way, which is currently being funded by DEP. Then using subsequent modeled nutrient data, compiled environmental, and reef monitoring data to conduct machine learning models of the relationships between factors relating to reef health for both corals and fishes (phase 2). This would provide a deeper understanding of the factors affecting reef health and the ability to target high impact mitigative actions and restoration strategies