The extensive change in climate is disrupting the ecosystem by impacting the aquatic flora and fauna. This poses critical challenges for biodiversity conservation and threatens the livelihood of the global human communities that depends on it. The changes in global climate in terms of rise in temperature, altered precipitation patterns, and sea level rise cause major shifts in the aquatic ecosystem by accelerating metabolic rates, altered growth, migration patterns, and reproductive cycles of aquatic species. Ocean acidification and changes in dissolved oxygen levels threaten coral reefs and other sensitive habitats, reducing species diversity and altering food webs. Climate change further exacerbates the spread of exotic species, upsetting aquatic ecosystems. Ecosystem dynamics and community composition are also changing as a result of several species moving into cold aquatic zones impacting several aspects of food security, fisheries, and biodiversity conservation. According to the projected climate forecasts, the resilience of aquatic ecosystems is expected to decline, amplifying the risk of ecosystem collapses and financial difficulties for dependent populations. The present chapter focuses on the effect of climate change on the aquatic flora and fauna, highlighting their distribution importance and present status. Future implications of these impacts on aquatic ecosystems were also discussed in this chapter along with the urgent need for adaptive conservation measures with quick mitigation and adaption plans.