2020 water quality data collected on a weekly basis using a YSI EXO2 multiparameter sonde and Secchi disk at 8 sites within or offshore of Bahia Almirante, a semi-enclosed tropical embayment on the Caribbean coast of Panama. Data were collected through the MarineGEO Bocas del Toro observatory (Bocas del Toro Research Station, Smithsonian Tropical Research Institute [STRI], Panama). Site locations: Colon: 9.386916, -82.211083 Hospital Point: 9.333416, -82.227166 Cristobal: 9.304166, -82.298611 Pastores: 9.210000, -82.326944 Almirante: 9.261694, -82.361833 Punta Caracol: 9.348388, -82.324888 Boca del Drago: 9.422900, -82.339400 STRI: 9.348611, -82.266111 Data were evaluated by MarineGEO technicians for quality assurance and quality control by removing all observations that were suspect or were not part of the sonde cast. These observations included data with salinity < 20 ppt, data from the first 30 seconds of the sonde cast (due to sonde acclimatization), and data from the sonde resting at the bottom of the bay. There may be cases where not all 8 sites were able to be sampled during a sampling period due to weather conditions. NA data were also unable to be collected. DESCRIPTION OF FILES INCLUDED IN THE DATA PUBLICATION data_2020_weekly-water-quality_PAN-BDT.csv: Data collected on a YSI EXO2 multiparameter sonde on a weekly basis at each of 8 sites. dictionary_2020_weekly-water-quality_PAN-BDT.csv: This file includes both the unit and description of all parameters.