Fishing activities are an important economic resource in the Paranaguá Bay, southern Brazil. In this area, there are reports of sea turtles interacting with small-scale fisheries. It was found that the juvenile green-turtle (Chelonia mydas) uses areas disturbed by fishing activity, which puts them at a higher risk of capture. The objective of this study was to evaluate the interactions of juvenile green-turtles with the gillnets used in small-scale fisheries, enabling a long-term understanding of those gillnet characteristics which increase the risk of turtle captures. The highest sea turtle capture rates occur in the early dry season, which is correlated with the larger displacement of individuals searching for available food sources. High levels of fishing effort also occur in this early dry period without a specific target resource. The highest levels of sea turtle mortality were observed during the coldest periods of the year (late rainy and early dry seasons) and can be related to the physiological needs of the sea turtles. The characteristics of gillnets that had the strongest relationships to turtle captures were soak time and mesh size. These results suggest that it is necessary to design new regulations governing aspects of fishing techniques such as soak time, net length or seasonal use of nets. Conservation initiatives aiming to reduce the risk of turtle capture must consider the economic importance of small-scale fishing practices and address the conflict that may exist between social concerns and environmental issues.