Direct consequences of biological invasions on biodiversity and the environment have been largely documented. Yet collateral indirect effects mediated by changes in agri-environmental policies aimed at combating invasions remain little explored. Here we assessed the effects of recent changes in water management in rice farming, which are aimed at buffering the impact of the invasive apple snail ( Pomacea maculata, Lamarck) on greenhouse gas emissions and diversity of waterbird communities. We used observational data from a 2-year field monitoring (2015–2016) performed at the Ebro Delta regional scale. We found that drying rice fields reduced methane emission rates by 82% (2015) and 51% (2016), thereby reducing the contribution of rice farming to climate change. However, there was a marked reduction (75% in 2015 and 57% in 2016) in waterbird diversity in dry fields compared with flooded fields, thus suggesting that post-invasion policies might hinder biodiversity conservation. Our results highlight the need for accounting for potential collateral effects during the policy decision-making process to design efficient agricultural management plans that lessen undesirable agri-environmental outcomes.