Estuaries have been under sampled to establish them as sources or sinks of the atmospheric carbon dioxide. Such poor coverage is well known for tropical, particularly monsoon driven, estuaries. In an attempt to study the variability in CO2 in a tropical monsoon estuary we made systematic time‐series observations in the Gautami Godavari estuarine system in the east coast of India. Our 18 month‐long extensive monitoring in the tropical Godavari estuarine system revealed pH >7.8 during dry period that decreased by 1.5 ± 0.01 during peak discharge period. The decrease in pH was associated with high nutrients and bacterial activities suggesting significant organic carbon decomposition. High bacterial respiration (20.6 ± 7.2 μMC l−1 d−1) in the estuary resulted in very high pCO2 of ∼30,000 μatm during peak discharge period, which otherwise were <500 μatm during dry period. Such high pCO2 levels were unknown to occur in any aquatic region. Several major and minor estuaries flow into the northern Indian Ocean from the Indian subcontinent and the monsoon associated processes make these systems chimney for emitting CO2 to atmosphere unrealized hitherto.

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