Migratory fishes are one of the groups most threatened by the interruption of river connectivity caused by reservoirs and dams. The downstream displacement of eggs and larvae of these species implies overcoming the barrier presented by the reservoir and passage through the hydraulic structures of the dam. Although a low water renewal time attenuates the drift constraints on eggs and larvae in the reservoir, these organisms still require safe passage through these structures, which represents an additional challenge that demands methodological tools for impact assessment and management evaluation to subsidise operational decision making. This paper presents a protocol to help fill current gaps in knowledge of the impact of hydropower dams on the survival of fish larvae travelling through the hydraulic components of dams. A sampling and analysis design capable of in situ assessment of the effects of passage by the larvae through dams is presented and discussed along with potential alternatives to support hydraulic structure management and mortality reduction as well as inferences on the effectiveness of fish translocation strategies. The proposed approach is a new possibility for the in situ assessment of downstream ichthyoplankton passage through dams. The proposed sampling design is relatively simple, easily executed and affordable compared to those demanding more sophisticated technologies or that combine field and lab studies to associate fish injuries and mortality with the downstream passage through dams operating under different regimes. Its rapid diffusion is important given the accelerated expansion of the hydroelectric sector, especially in the main tropical basins.