Phosphorites can record oceanic conditions during their deposition, but the faithful retention of primary information in Paleoproterozoic deposits can be mitigated by post‐depositional processes. Here, we examine a peritidal phosphorite within a microbialite reef complex in the 2.4–2.2 Ga Turee Creek Group in Western Australia to assess the environmental information retained. Field mapping and petrography distinguishes between authigenic and locally transported phosphorite fragments, each of which contains unique information regarding the deposit. Elemental mapping and laser‐ablation analyses differentiate the impact of depositional versus early diagenetic versus metamorphic processes within these fragments. Samples within a near‐shore pebble conglomerate have mixed riverine‐oceanic signals and lack cerium anomalies, consistent with the depositional environment. Clasts from off‐shore peloidal grainstone beds retain “hat‐shaped” patterns with small negative cerium anomalies, reflective of transport and redeposition within potentially oxic seawater. U‐Pb isotopic dates range from ∼1.8 to 2.3 Ga and are generally uncorrelated with rare earth element and yttrium data. The youngest date (∼1.8 Ga) is associated with recrystallized apatite, with concave down, middle rare earth element enriched patterns. A potential depositional age, ∼2.3 Ga, is associated with massive apatite in a chert‐rich clast that has rare earth element patterns reflective of riverine‐oceanic signals. Overall, the peritidal system in the reef was dynamic, with potentially oxic seawater that had a strong riverine influence. Local recycling and reworking, early diagenesis, and later orogenic events impacted the preserved geochemical signals and together show that spatially resolved geochronological and geochemical data are ideal for interpreting ancient phosphorites. Plain Language Summary Understanding our ancient rock record is challenging because very few rocks are preserved from early Earth. Phosphorites are sedimentary deposits that are useful environmental archives because apatites can preserve primary chemical information. Here, we examined a shallow water phosphorite deposit from a reef complex in the c. 2.4–2.2 Ga Turee Creek Group to see what information is preserved. Knowing what the environment was like at this time will provide important insights into life at the time of the Great Oxidation Event. The phosphorite here contains a variety of textures of apatite, representative of different environmental and secondary processes, so we used spatially resolved techniques to study the different textures. Our data show that more chemically pristine apatite textures record a potentially oxic, mixed riverine‐oceanic signal, while others are more representative of transport and early diagenesis or metamorphism. Overall, we show that deep‐time phosphorites are useful archives for environmental information and that life at this time may have encountered oxygenated water in the very shallow oceans. Key Points Spatially resolved data differentiate depositional and secondary information from a peritidal phosphorite in a Paleoproterozoic microbialite reef complex Apatite rare earth element data indicate a mixed riverine‐oceanic, potentially oxic signal for the depositional environment Apatite U‐Pb data show a prospective depositional/early diagenetic age (∼2.3 Ga) alongside ages coincident with regional orogenic events at ∼2.1 and ∼1.8 Ga