Puerto Rico Coral Reef Monitoring Program Water Quality Data from 2023–2025

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Scientific Data volume 13, Article number: 150 (2026) Cite this article

Abstract

Coral reefs are declining due to a combination of global and local anthropogenic stressors. While water quality is an important driver of coral reef condition, the lack of systematic water quality monitoring efforts has prevented a more thorough analysis of the role of water quality parameters in modulating coral reef declines. Here we present 8,032 measurements representing seawater temperature, salinity, dissolved oxygen, pHNBS, Secchi depth, CO2 chemistry (dissolved inorganic carbon and total alkalinity), biological oxygen demand (BOD), total suspended solids, settleable solids, turbidity, chlorophyll-a, ortho-phosphate, nitrite + nitrate (NOx), total Kjeldahl nitrogen (TKN), and Enterococcus spp. from 42 Puerto Rico coral reef sites from 2023 to 2025. These data provide a critical baseline for coral reef water quality that can be used to develop and assess water quality thresholds, explore spatiotemporal variability in seawater chemistry, ground truth remote sensing observations, and downscale earth system models to improve global monitoring efforts and projections for coral reefs under ongoing anthropogenic impacts.

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Background & Summary

Coral reefs provide a range of ecosystem goods and services to humans worldwide1. However, mean coral cover has declined from 34.8% to just 16.3% from 1969 to 2011 while macroalgal cover increased from 7% to 23.6% during that same period2. Consequently, there are increasing concerns that coral reefs across the Caribbean are flattening3, may be unable to keep up with sea level rise4,5, and are decreasing their provisioning of ecosystem services1,6. Disease outbreaks, tourism, overfishing, and warming have been implicated as the primary drivers of declining Caribbean coral reef condition2. While sedimentation, heavy metals, herbicides, turbidity, nutrients, sewage, runoff, and fluvial inputs can also affect coral reef organisms and communities7,8,9,10, sparse water quality data has prevented a more robust analysis of its impacts on Caribbean coral reefs2.

In this study, we conducted eight quarterly water quality surveys from all of the Puerto Rico Coral Reef Monitoring Program (PRCRMP) sites from 2023–2025 for seawater temperature, salinity, dissolved oxygen, pHNBS, Secchi depth, CO2 chemistry (dissolved inorganic carbon and total alkalinity), biological oxygen demand (BOD), total suspended solids, settleable solids, turbidity, chlorophyll-a, ortho-phosphate, nitrite + nitrate (NOx), total Kjeldahl nitrogen (TKN), and Enterococcus spp. The PRCRMP was established in 1999 to monitor the benthic community composition and fish assemblages for selected coral reef sites ranging from 5 m to 30 m depth but have not been previously surveyed for water quality parameters (Fig. 1). To our knowledge, this data provides the first comprehensive snapshot of coral reef water quality across the Puerto Rico archipelago that can be used for a wide range of applications while serving as a baseline from which to evaluate future change.

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https://www.nature.com/articles/s41597-025-06468-6

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