Neotropical calcium carbonate (CaCO₃)-forming streams (travertine streams) are biodiversity hotspots with high biological production. Phosphorus (P) is a key nutrient for gross primary production (GPP), but CaCO₃ precipitation reduces its availability through co-precipitation, exacerbating P limitation and affecting GPP and ecosystem respiration (ER). A critical question arises: how do these P-limited systems sustain GPP? One hypothesis is that dense fish aggregations recycle nutrients via excretion, alleviating P limitation and supporting primary producers. Since GPP and ER fluctuations may drive CaCO₃ precipitation and dissolution, respectively, understanding these processes is essential. We investigated how stream metabolism influences CaCO₃ precipitation and evaluated fish as nutrient recyclers. We predict that (1) fish play a crucial role in meeting autotrophic nutrient demands as P limitation increases with precipitation and (2) precipitation rises in less heterotrophic streams due to GPP offsetting. We quantified fish densities using depletion methods and visual surveys, measured fish excretion rates, and assessed whole-reach nutrient limitation through pulse experiments. High-frequency in situ data loggers captured diel changes in dissolved oxygen, light, temperature, and calcium, allowing inverse modeling to estimate GPP, ER, net ecosystem production (NEP), and CaCO₃ precipitation rates. Results showed that reduced P availability and shorter P uptake lengths were associated with high CaCO₃ deposition rates, indicating P limitation. However, high fish aggregations increased nutrient fluxes and supported GPP, corroborating our first hypothesis. Streams were net heterotrophic, but high GPP enhanced CaCO₃ deposition by 50–75%, offsetting dissolution effects. NEP correlated negatively with net CaCO₃ deposition, suggesting that as streams become less heterotrophic, CaCO₃ precipitation increases. Our findings highlight the role of animals and pooled microbial communities in driving CaCO₃ formation, with microbial metabolism enhancing chemical reactions and animals creating biogeochemical hotspots, underscoring the need to integrate biology and geochemistry in stream models.