Humans have dramatically increased phosphorus (P) availability in terrestrial and aquatic ecosystems. As P is often a limiting nutrient of primary production, changes in its availability can have dramatic effects on ecosystem processes. I examined the effects of calcium carbonate (CaCO3) deposition, which can lower P concentrations via coprecipitation of phosphate, on P availability in two systems: streams in the Huachuca Mountains, Arizona, and a stream, Río Mesquites, in Cuatro Ciénegas, México. Calcium carbonate forms as travertine in the former and within the microbialites of the latter. Despite these differences, CaCO3 deposition led to lowered P availability in both systems. By analyzing a three-year dataset of water chemistry from the Huachuca Mountain streams, I determined that P concentrations were negatively related to CaCO3 deposition rates. I also discovered that CaCO3 was positively correlated with nitrogen concentrations, suggesting that the stoichiometric effect of CaCO3 deposition on nutrient availability is due not only to coprecipitation of phosphate, but also to P-related constraints on biotic nitrogen uptake. Building from these observations, bioassays of nutrient limitation of periphyton growth suggest that P limitation is more prevalent in streams with active CaCO3 deposition than those without. Furthermore, when I experimentally reduced rates of CaCO3 deposition within one of the streams by partial light-exclusion, areal P uptake lengths decreased, periphyton P content and growth increased, and periphyton nutrient limitation by P decreased. In Río Mesquites, CaCO3 deposition was also associated with P limitation of microbial growth. There, I investigated the consequences of reductions in CaCO3 deposition with several methods. Calcium removal led to increased concentrations of P in the microbial biomass while light reductions decreased microbial biomass and chemical inhibition had no effect. These results suggest that CaCO3 deposition in microbialites does limit biological uptake of P, that photoautotrophs play an important role in nutrient acquisition, and, combined with other experimental observations, that sulfate reduction may support CaCO3 deposition in the microbialite communities of Río Mesquites. Overall, my results suggest that the effects of CaCO3 deposition on P availability are general and this process should be considered when managing nutrient flows across aquatic ecosystems.