Understanding processes involved phosphorus (P) cycling in the soil-water continuum requires novel techniques that can that go beyond operationally defined methods and can connect sources, chemical reactivity, and pathways of transformation. Here we present a series of recent research efforts aimed to address these questions using HPIC, HPLC-MS, NMR, NanoSIMS, Bayesian modeling, and stable isotope methods in an agriculture-runoff dominated catchment. Our data show dynamic variability of P speciation, influenced primarily by runoff and tides, with phytate being the dominant form of P. Distinct sets of isomers and isotopically identical phosphate moieties in phytate prove IRMS as a reliable tool to track the sources of phytate. Isotope composition of P pools and fingerprinting element modeling allow tracking sources of P in the downstream water. The abundance of bacteria capable of phytate degradation and expression of phytate genes indicate that the presence of phytate promotes the proliferation of phytate-degrading microorganisms. Similarly, the nanoSIMS method of measuring in-situ isotopes is being investigated. While a scrutiny is needed to connect results from different techniques, new analytical methods have enabled improved understanding of micro- to macro-level P process in soils and waters.