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The current paper aims to develop and to apply a methodology for assessing the hydroenergy harvesting potential in water systems taking into account both technical and economic aspects. The methodology is a five-step procedure: (i) data collection and analysis; (ii) technology identification; (iii) energy harvesting assessment; (iv) economic analysis; and (v) final recommendation of the technological solution. The case study is located in the water source of the Alviela River, in Portugal. The energy harvesting potential is assessed for three turbine types, adequate for the 2.5 m available head: two propeller turbines, with and without adjustable blades, and the Archimedes screw turbine. Results show that the most feasible solution is the Archimedes screw turbine, with 3 m<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mn>3</mn></msup></semantics></math></inline-formula>/s rated discharge and 55 kW rated power, the capital cost of 160 k€, the internal rate of return above 10% and the payback period of eight years. This solution has the potential for harvesting energy in low-head sites with a wide range of flow rates.