Fieldwork within the Paute river basin is an important element of the HydroCORE project. The river basin is characterised by two main reservoirs: Mazar and Amaluza. Mazar lies upstream of Amaluza and is fed by the rivers Paute (originating from the city of Cuenca) and Collay, while Amaluza is mostly fed by the effluent of Mazar. Within this river basin, 20 reservoir sites and 19 river sites are selected. In addition, a similar river basin without hydropower infrastructure is used as a reference situation. For this, the headwaters of the Jubones river are selected and sampled through 11 sites.

At each location, the physical characteristics (e.g., flow velocity, land use, weather conditions) are noted by means of a field protocol. The chemical conditions (e.g., temperature, dissolved oxygen, pH) are recorded in situ through a multiprobe, while samples are collected for nutrient analysis in the laboratory (e.g., nitrate, nitrite, ammonium). The biological characteristics are determined through the sampling of the macroinvertebrate assemblage by means of a hand net (25 x 25 cm², 500 μm mesh size) and the inspection of a selection of stones. The emission of greenhouse gases is determined by using a floating chamber and measuring the internal air composition at three fixed time points (0 - 20 - 40 mins), complemented with a sample of the dissolved gases.

Data is collected at a regular basis, with abiotic conditions being registered four times a year and biotic conditions being registered two times a year. As a result, the HydroCORE project foresees a total of eight sampling campaigns: