Elemental cycles are coupled directly and indirectly to ecosystem metabolism at multiple time scales. Understanding coupling in lotic ecosystems has recently advanced through simultaneous high-frequency measurements of multiple solutes. Using hourly in situ measurements of soluble reactive phosphorus (SRP), specific conductance (SpC), and dissolved oxygen (DO), we estimated phosphorus (P) retention pathways and dynamics in a large (discharge, Q ≈ 7.5 m3/s) spring-fed river (Ichetucknee River, Florida, USA). Across eight multi-day deployments, highly regular diel SRP variation of 3–9 μg P/L (mean 50 μg P/L) was strongly correlated with DO variation, suggesting photosynthetic control directly via assimilation, and/or indirectly via geochemical reactions. Consistent afternoon SRP maxima and midnight minima suggest peak removal lags gross primary production (GPP) by 8 hours. Two overlapping processes were evident, one dominant with maximum removal near midnight, the other smaller with maximum removal near midday. Hourly [Ca] measurements during three 24-hour deployments showed consistent afternoon minima, suggesting that calcite precipitates as GPP increases pH and mineral saturation state. Resulting P co-precipitation was modeled using SpC as a [Ca] proxy, yielding a diel P signal adjusted for the primary geochemical retention pathway. P assimilation, the dominant diel signal, was computed by interpolating between daily concentration maxima, both with and without geochemical adjustment, and converting concentration deficits to fluxes using discharge and benthic area. Adjusting for calcite co-precipitation yielded assimilation rates (13.7 ± 5.8 mg P·m−2·d−1) strongly correlated with GPP, accounting for 72% ± 9% of gross removal, and ecosystem C:P stoichiometry (466 [± 12]:1) consistent with dominant vascular autotrophs (478 [± 24]:1). Without adjusting for co-precipitation, covariance with GPP was weaker, and C:P implausibly high. Consistent downstream P accumulation, likely from P-rich porewater seepage, varied across deployments (3–22% of total flux) and co-varied with discharge and respiration. Asynchronous N and P assimilation may arise from differential timing of protein and ribosome production, with the latter requiring maximal carbohydrate stores and minimal photolytic interference. This study demonstrates direct and indirect coupling of biological, hydrological, and geochemical processes and the utility of high-resolution time series of multiple solutes for understanding these linkages.