This study proposes an innovation, which is to use a non-circular and bio-inspired forced conduit (a new penstock with a cross section inspired by a tree trunk), to control the effects of hydraulic transients in Brazilian small hydropower plants (SHPs). The aim is to demonstrate that natural structures, adapted to periodic environmental disturbances, are better at hydraulic transient control than traditional conduits. The proposed methodology includes the following steps: (1) problem identification; (2) potential biological model identification; (3) development of alternatives; (4) implementation and testing; and (5) solution selection. This research was conducted at the São Tadeu I SHP, in the city of Santo Antônio de Leverger/MT, Brazil. The following tree biological models from the Brazilian savannah (Cerrado) were used: Handroanthus capitatus and Strychnos pseudoquina. The proposed innovation improves the conduit of the traditional circular section and the relief valve solution of the criteria studied. The reason for this improvement was the reduction of wave speed in the non-circular section (from 1126 to 583 m s−1).