Over the period 2016–2022 environmental data were obtained at four points in the northern section of the tropical Estero Salado (ES), the inner coastal lagoon that flows through Guayaquil, the largest city in Ecuador. Surface water from the more remote southern limit of the ES, El Morro was also sampled in 2022. The study shows that waters of the northern part of this low salinity (<12) coastal lagoon were often hypoxic, occasionally approached anoxia, and were slightly acidic (6.86 ± 0.67). The same waters contained extremely high concentrations of dissolved inorganic nitrogen which averaged between 2.00 and 16.3 μM for nitrite, 89.8–238 μM for nitrate and 35.0–758 μM for ammonium whilst dissolved inorganic phosphorus averaged 21.3–381 μM. Dissolved oxygen was between 22.4 and 129 μM, and all samples were <50% saturated. Additionally, remarkably high concentrations of total and fecal coliforms and Escherichia coli were measured in this northern section, which are well above national and international standards. A trophic state index strongly indicates that northern part of the ES is hyper-eutrophic. Whilst nutrients were at lower concentrations at El Morro, they still exceeded those expected for typical natural and balanced estuaries, thus showing signs of eutrophication. Two major drivers for these hyper-eutrophic conditions in the north are effectively no riverine inputs to flush the system, and nutrient inputs being dominated by run off from the city as industrial, wastewater and sewage discharges, together with pulses associated with the seasonal rainfall. Based on comparison of nutrient data given here with the same parameters from several decades ago, the situation has become worse over this timescale. This trend follows the dramatic increase in population of the city of Guayaquil, and associated increase in discharges of polluted waters. The ES needs major improvements in environmental quality if it is to avoid further deleterious impacts for local populations. The ES thus fits into the global trend of increasing eutrophication in estuarine and coastal waters. Estimates using the new nutrient measurements indicate that the ES is exporting significant amounts of DIN and DIP into coastal waters of the Gulf of Guayaquil and then the Eastern South Pacific.