Shipping is regarded as an important vector for aquatic non-indigenous species (ANIS) worldwide. Less attention has been paid to its role in relation to environmental and economic causes of introduction and establishment, the knowledge of which is necessary to assess effects of changes in regulations on shipping. The purpose of this study was to estimate the impact of shipping on the incidence of ANIS in the Baltic Sea compared with environmental and economic factors. To this end, a production function was estimated with count data on ANIS (response variable) and shipping, environmental and economic factors as explanatory variables. Regression results from different regression models showed that shipping has a significant impact on ANIS incidence and can account for up to 38% of the number of ANIS in the sea. Predictions of the impact of measures implementing the Convention for the Control and Management of Ships' Ballast Water and Sediment indicated a reduction by 17% in the number of ANIS, which was counteracted by an expected increase in shipping traffic. © 2022