This record provides physical and chemical water quality metrics collected between February 2023 to January 2025 to provide reference data of nearshore and watershed water quality on the island of Culebra, Puerto Rico. The water quality monitoring was conducted at 18 fixed stations. Five stations were selected to quantify Land Based Sources of Pollution (LBSP) stressor loads at key points in the Cabra, Coronel, and Aeropuerto watersheds. Levels of LBSP exposure were measured at 13 nearshore stations co-located with long-term seagrass monitoring sites. Nearshore monitoring sites were selected to identify watershed discharge points, coastal hydrodynamics, as well as the existing level of LBSP exposure and anticipated changes to LBSP exposure due to management actions. Nearshore monitoring stations were designated based on their land based sources of pollution (LBSP management implementation status (LBSP Treatment Group), as follows: 1) LBSP Restoration stations: Located downstream where land-based pollutant management has or is being implemented. 2) LBSP Control stations: Represent a range of land-based pollutant impairments, including sites with no LBSP management, no known direct discharge of LBSP but are representative of the range of external factors that may be encountered at the LBSP Restoration stations. 3) Negative Reference stations of know significant -anecdotal and quantified- LBSP impairment. 4) Positive Reference stations of low LBSP impairment. Nearshore water quality parameter measurements were collected at two depths: surface (10-25 cm ) and bottom (2 m deep). Metrics include: 1. Water physical properties: Temperature, Salinity, Dissolved Oxygen, and pH. 2. Indicators of water clarity threats: CDOM (Colored Dissolved Organic Matter), absorbs light in the blue and UV part of the electromagnetic spectrum giving water a yellow-brown color; Turbidity; Chlorophyll-a, used to gain insight of phytoplankton primary productivity, measured as the blue fluorescence emission; and Kd-PAR, the Attenuation coefficient of Photosynthetic Active Radiation. 3. Indicators of wastewater threats: Optical brighteners, which are whitening agents added to laundry soaps, detergents, toilet paper, and cleaning products to brighten fabrics and/or surfaces, are used to detect the presence of household effluent; and Monochloramines, long-lasting disinfectant used to treat drinking water protecting its quality as it moves through distribution pipes, primarily serving as a marker for the effectiveness of water treatment. 4. Indicators of fecal contamination: Fecal coliforms, the group of bacteria found in fecal matter from warm-blooded animals, including humans; Enterococcus, the group of fecal coliforms specifically used to assess water quality in marine and estuarine environments; and E. coli, a specific type of fecal coliform often considered a more reliable indicator due to its specific association with human waste. The data presented herein was collected with financial support from NOAA Restoration Center and NOAA Coral Reef Conservation Program, and the National Fish and Wildlife Foundation (NFWF).