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Rivers act as a natural source of greenhouse gases (GHGs). However, anthropogenic activities can largely alter the chemical composition and microbial communities of rivers, consequently affecting their GHG production. To investigate these impacts, we assessed the accumulation of CO2, CH4, and N2O in an urban river system (Cuenca, Ecuador). The study area is located at the Cuenca River basin situated in the southern province of Azuay in the Andes of Ecuador. The basin is composed of five main tributaries, i.e. Cuenca, Tarqui, Yanuncay, Tomebamba, and Machangara Rivers. The study area is 572.92 km2, representing 25% of the Cuenca River basin. A sampling campaign was conducted in September 2018. During this period, samples were collected from 9.00 to 18.00. 36 sites were sampled in the Cuenca river basin, splitting into the five basins covering the whole urban river area as well as the river sources. Besides assessing the dissolved concentrations of CO2, CH4, and N2O, we also gathered physiochemical, hydro-morphological, and meteorological data. Specifically, water temperature, pH, dissolved oxygen (DO), turbidity, total dissolved solid (TDS), and chlorophyll a were determined by a handheld multiprobe (Aquaread-AP5000 version 4.07). Calibration was performed prior to sampling and supplemented with a regular check after sampling.

Water samples from all sampling sites were collected and stored in cool and dark containers and then preserved in a refrigerator before being analyzed for other variables in the Water and Soil Quality Analysis Laboratory at Cuenca University. Particularly, ammonium (NH4+), nitrite (NO2-), nitrate (NO3-) and orthophosphate (PO43-) were determined spectrophotometrically (low-range Hach test kits with Hach DR3900). Moreover, water samples were kept frozen until shipment to Belgium for further analyses, i.e. biochemical oxygen demand (BOD5), chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP). Details of the Hach kits can be found in Supporting Information (SI) S1. Hydro-morphological information of the sites and their surroundings were collected, including land use, macrophytes, riparian vegetation, channel types, and sediment accumulation, via a modified field protocol of Ruben Jerves-Cobo et al. (2018). Note that land-use types surrounding the sampling sites were assessed using the modified field protocol based on the Australian River Assessment System physical assessment protocol (Parsons et al., 2002) and the United Kingdom and the Isle of Man River Habitat Survey (Raven et al., 1997). In total, 17 variables were measured following different categories (SI S2). River depth and velocity were measured at three points at each sampling site, two close to the riverbanks and one in the middle of the river. Meteorological data, including air temperature, solar radiation, rainfall, and wind speed, were obtained from the meteorological station of the University of Cuenca (-2.9050372degree, -79.0124267degree), located 7.8 km away from the Ucubamba WWTP and 0.7 km away from the city center.