Tayrona National Natural Park (TNNP) is a hotspot of coral reef biodiversity in the Colombian Caribbean, located between the city of Santa Marta (>455,000 inhabitants) and several smaller river mouths (Rio Piedras, Mendihuaca, Guachaca). The region also experiences a strong seasonal variation in physical parameters (temperature, salinity, wind, and water currents) due to alternating dry seasons with coastal upwelling and rainy seasons. However, the spatial and temporal effects on water quality parameters relevant for coral reef functioning have not been investigated. Therefore, inorganic nutrient, chlorophyll a, and particulate organic carbon (POC) concentrations along with biological O2 demand (BOD), pH, and water clarity directly above local coral reefs (~10 m water depth) were monitored for 25 months in four bays along a distance gradient (12-20 km) to Santa Marta in the southwest and to the first river mouth (17-27 km) in the east. This is by far the most comprehensive coral reefs water quality dataset for the region. Findings revealed that particularly during non-upwelling, chlorophyll a and POC concentrations along with BOD significantly increased with decreasing distance to the rivers in the east, suggesting that the observed spatial water quality decline was triggered by riverine runoff and not by the countercurrent-located Santa Marta. Nitrate, nitrite, and chlorophyll a concentrations significantly increased during upwelling, while pH and water clarity decreased. Generally, water quality in TNNP was close to oligotrophic conditions adequate for coral reef growth during non-upwelling, but exceeded critical threshold values during upwelling and in relation to riverine discharge.