Dissolved nutrient dynamics broadly affect issues related to public health, ecosystem status and resource sustainability. Modeling ecosystem dynamics and predicting changes in normal variability due to potentially adverse impacts requires sustained and accurate information on nutrient availability. On site sampling is often resource limited which results in sparse data sets with low temporal and spatial density. For nutrient dynamics, sparse data sets will bias analyses because critical time scales for the relevant biogeochemical processes are often far shorter and spatially limited than sampling regimes. While data on an areal basis will always be constrained economically, an in-situ instrument that provides coherent data at a sub-tidal temporal scale can provide a significant improvement in the understanding of nutrient dynamics and biogeochemical cycles. WET Labs has developed an autonomous in-situ phosphate analyzer which is able to monitor variability in the dissolved reactive phosphate concentration (orthophosphate) for months with a sub-tidal sampling regime. The CYCLE phosphate sensor is designed to meet the nutrient monitoring needs of the community using a standard wet chemical method (heteropoly blue) and minimal user expertise. The heteropoly blue method for the determination of soluble reactive phosphate in natural waters is based on the reaction of phosphate ions with an acidified molybdate reagent to yield molybdophosphoric acid, which is then reduced with ascorbic acid to a highly colored blue phosphomolybdate complex. This method is selective, insensitive to most environmental changes (e.g., pH, salinity, temperature), and can provide detection limits in the nM range. The CYCLE sensor uses four micropumps that deliver the two reagents (ascorbic acid and acidified molybdate), ambient water, and a phosphate standard. The flow system incorporates an integrated pump manifold and fluidics housing that includes controller and mixing assemblies virtually insensitive to bubble interference. A 5-cm pathlength reflective tube absorption meter measures the absorption at 880 nm associated with reactive phosphate concentration. Reagents and an on-board phosphate standard for quality assurance are delivered using a novel and simple-to-use cartridge system that eliminates the user's interaction with the reagents. The reagent cartridges are sufficient for more than 1000 samples. The precision of the CYCLE sensor is ~50 nM phosphate, with a dynamic range from ~0 to 10 μΜ. The CYCLE sensor operates using 12 VDC input, and has a low current draw (milliamps). CYCLE also has 1 GB on-board data storage capacity, and communicates using a serial interface. The host software for the CYCLE sensor includes a variety of features, including deployment planning and sensor configuration, data processing, plotting of raw and processed data, tracking of reagent usage and a pre and post deployment calibration utility. The instrument has been deployed in a variety of sampling situations: freshwater, estuarine, and ocean. Deployments are typically for over 1000 samples worth of continuous run time without maintenance (4–12 wks). Using the CYCLE phosphate sensor, a sufficient sampling rate (~20–30 minutes per sample) is realized to monitor in-situ nutrient variability over a broad range of time scales including tidal cycles, runoff events, and phytoplankton bloom dynamics. We present a time series of phosphate data collected in Yaquina Bay, Oregon. Combining this data with complimentary measurements, the CYCLE phosphate provides a missing link in understanding nutrient dynamics in Yaquina Bay. We demonstrate that by correlating phosphate variability with nitrate, chlorophyll, dissolved oxygen, turbidity, CDOM, conductivity, and temperature, a greater understanding of the factors influencing nutrient flux in the bay is possible. What nutrients limit production and whether anthropogenic or oceanic sources of nutrients dominate bloom dynamics can be explored. This work demonstrates the importance of in-situ, frequent, and long-term monitoring to better understand the nutrient and bloom dynamics in estuaries. It suggests that with more extensive phosphate networks, the impacts of anthropogenic nutrient loading in estuaries and coastal system could be assessed.