The construction of large infrastructure projects, such as railways, can cause significant impacts on aquatic ecosystems, especially in semiarid regions where soils are more vulnerable to erosion and desertification. This study evaluated the effects of the construction of the West-East Integration Railway on the limnology and zooplankton community of the Pedra Reservoir, located in the Brazilian semiarid region. We analyzed three periods-before, during, and after the railway construction-considering physical and chemical water variables as well as zooplankton diversity. Response variables were evaluated using both univariate and multivariate methods. The results indicated that the railway construction altered water quality, increasing turbidity and suspended solids during the construction period, which negatively impacted the zooplankton community, reducing species richness, density, and diversity. Although signs of resilience were observed in the postconstruction period, the zooplankton community has not fully returned to its previous state. This study highlights the importance of strategic planning in large-scale projects, emphasizing the need to avoid interventions near water bodies and implement mitigation measures such as erosion control and revegetation of margins. Such actions are essential to preserve environmental integrity in semiarid ecosystems, which are highly vulnerable to climate change and eutrophication processes.