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Abstract Marine organisms are increasingly recognized as both responding to and driving biogeochemical changes in their environment. The addition of exogenous resources to the ocean, such as nutrients, that alter organismal physiology can lead to biogeochemical cascades wherein these solutes both alter water chemistry directly and indirectly by changing biological processes that influence water chemistry. To quantify how allochthonous nutrients drive biogeochemical cascades, we measured a suite of biogeochemical parameters during synoptic spatial surveys across two reefs in Mo’orea, French Polynesia conducted day and night at both low and high tide in two different seasons. These data were used to build a model that demonstrates how inputs of nutrients to coral reefs via submarine groundwater discharge directly alter reef metabolism with cascading effects on the cycling of dissolved organic and inorganic carbon that regulate productivity, calcification, and the microbial loop. 

The addition of terrestrial inputs to the ocean can have cascading impacts on coastal biogeochemistry by directly altering the water chemistry and indirectly changing ecosystem metabolism, which also influences water chemistry. Here, we use submarine groundwater discharge (SGD) as a model system to examine the direct geochemical and indirect biologically mediated effects of terrestrial nutrient subsidies on a fringing coral reef. We hypothesize that the addition of new solutes from SGD alters ecosystem metabolic processes including net ecosystem production and calcification, thereby changing the patterns of uptake and release of carbon by benthic organisms. SGD is a common land–sea connection that delivers terrestrially sourced nutrients, carbon dioxide, and organic matter to coastal ecosystems. Our research was conducted at two distinct coral reefs in Moʻorea, French Polynesia, characterized by contrasting flow regimes and SGD biogeochemistry. Using a Bayesian structural equation model, our research elucidates the direct geochemical and indirect biologically mediated effects of SGD on both dissolved organic and inorganic carbon pools. We reveal that SGD‐derived nutrients enhance both net ecosystem production and respiration. Furthermore, the study demonstrates that SGD‐induced alterations in net ecosystem production significantly influence pH dynamics, ultimately impacting net ecosystem calcification. Notably, the study underscores the context‐dependent nature of these cascading direct and indirect effects resulting from SGD, with flow conditions and the composition of the terrestrial inputs playing pivotal roles. Our research provides valuable insights into the interplay between terrestrial inputs and coral reef ecosystems, advancing our understanding of coastal carbon cycling and the broader implications of allochthonous inputs on ecosystem functioning.