Coastal wetlands face numerous threats from human activities, including habitat alteration for rice cultivation and contamination by agrochemicals. In this study, we evaluated the impact of different rice production practices on the structure of aquatic communities and greenhouse gas emissions in the Albufera Natural Park (Valencia, Spain), one of the most important Mediterranean coastal wetlands. We monitored the diversity of aquatic bacteria and archaea, zooplankton, and macroinvertebrates over the rice cultivation period at four sampling sites: a water spring representing a natural (unimpacted) area, an organic rice field, and two conventional rice fields. Additionally, we measured CO₂ and CH₄ emissions at various stages of the rice cultivation period. Our study shows that areas dedicated to ecosystem preservation, such as water springs, support a higher diversity of bacteria and archaea and provide habitat for endemic and endangered macroinvertebrate species. Moreover, these areas exhibit the lowest relative greenhouse gas emissions from the water column, offering significant benefits for climate change mitigation. The study also reveals that the structure of aquatic communities is heavily influenced by rice farming practices, with organic rice farming supporting a larger abundance of pollution-resistant zooplankton and a higher diversity and biomass of emerging insects. However, organic rice farming was associated with the highest prevalence of fecal microorganisms and contributed more to greenhouse gas emissions during the rice cultivation period due to its manure fertilization regime. These findings underscore the need to carefully consider both the benefits and challenges of different farming practices, balancing ecological conservation and GHG emissions with sustainable agricultural production.
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