Mangrove forests are among the most productive ecosystems globally, offering critical ecosystem services such as coastal protection, carbon sequestration, and support for mangrove-dependent fisheries. These forests host a diverse range of microorganisms that contribute to nutrient acquisition, disease resistance, and adaptation to salinity stress, yet many of these microbes remain uncharacterized. Mangrove forests are increasingly threatened by habitat loss,climate change, and pollution. The impact of these anthropogenic stressors on the microorganisms that sustain these forests, and on the local artisanal fishery communities, remains largely unknown. This research addresses the effects of land use changes, particularly nutrient pollution associated to shrimp aquaculture, on nutrient cycling, water quality, and microbial community function and structure. It also examines the variability and influence of mangrove zones and flow dynamics on microbial community structure and function in less perturbed mangrove forests. Additionally, this work investigates how salinity and pathogenic stress affect mangrove microbial communities and their functions and develops a model to explore plant-microbe interactions to understand how microbes could provide chemical protection to the plant to tolerate stress. Finally, this research focuses on developing methodologies to build just and equitable partnerships with local Afro-Ecuadorian communities to better understand the impact of pollution and threats to mangrove forests and mangrove-dependent fisheries. The findings of this work offer valuable insights for conservation efforts and provide a framework for addressing ecological challenges in vulnerable coastal regions to climate change.