Coastal waters in rapidly urbanizing regions face increasing threats from excessive nutrient and organic matter inputs, leading to eutrophication, habitat degradation, and harmful algal blooms. To address this issue, we conducted a comprehensive, year-long (August 2021–July 2022) nutrient monitoring study in Mombasa, Kenya representative city for developing coastal areas experiencing high population growth. Monthly surveys were carried out at geo-referenced sites, where environmental parameters such as temperature, salinity, dissolved oxygen (DO), and turbidity were measured in situ using a YSI Professional Plus Water Quality Meter (SKU6050000) and a Thermo Scientific™ Portable TN100 Turbidity Meter, respectively. Surface seawater samples were collected for dissolved inorganic nutrients, filtered immediately through 0.45 µm Sartorius Minisart® syringe filters, preserved with mercury chloride (50 µl of 20 g/L HgCl₂ per 100 ml), and stored cool until analysis. Pore water samples were also obtained during both dry and wet seasons. In the laboratory, concentrations of dissolved inorganic nutrients (nitrogen, phosphorus, silicates) were determined using spectrophotometry (Infinite® M200 NanoQuant, Tecan Group Ltd.) following standardized protocols Grasshoff et al., (2007). Submarine groundwater discharge (SGD) fluxes were estimated via radon isotope tracing using a Durridge RAD7 radon monitor alongside measurements of water parameters and meteorological data. All field sampling and measurements were performed in duplicate to ensure data quality, and geo-referencing was managed with KoboCollect v2022.2.3. This dataset provides critical insights into nutrient loading and its variability in tropical coastal environments, supporting future coastal management and research.