The maritime industry is currently experiencing a shift towards green corridors. The inland waterway is the main transportation corridor with a relatively low adoption of green technologies, which produces heavy air pollution in inland cities. This paper investigates the ship deployment problem for an inland river carrier considering the adoption of green fuel and green technologies for a given ship fleet. A non-linear programming (NLP) model is proposed to jointly optimize green technology adoption, sailing speed, and routing problems while considering two unique characteristics of inland river shipping, including the non-identical streamflow and the speed limits on each shipping leg. The analytical propositions reveal the optimal operation strategy of the inland river ship fleet, and a column generation-based algorithm is further designed to solve the proposed model. By jointly investigating the ship operation strategy and sulphur emissions, we find the following management insights: Firstly, the ship would have a lower willingness to invest in shore power (scrubber) if it installed scrubber (shore power). The higher streamflow and looser speed limits would reduce the spillover effect of green technology adoption. Secondly, emissions will spillover from ports to river legs if only shore power is provided. Our findings provide valuable insights for policymakers to promote complete green technology adoption to achieve comprehensive abatement of the entire inland river.